Uses of Interface
ambit2.base.interfaces.IStructureRecord

Packages that use IStructureRecord

Package	Description
ambit2.base.data	Base data structures; no chemistry.
ambit2.base.data.study	Detailed description of experimental data, linked to substances
ambit2.base.interfaces	Format independent IO utilities
ambit2.base.processors	Processors (similar to a processing node in a workflow engine)
ambit2.base.processors.search
ambit2.base.relation	Classes to describe relations between chemical structures
ambit2.base.relation.composition	Classes to describe chemical composition
ambit2.chebi
ambit2.core.io	Input output support.
ambit2.core.io.dx
ambit2.core.io.json
ambit2.core.io.pdb
ambit2.core.processors
ambit2.core.processors.structure
ambit2.core.processors.structure.key
ambit2.db
ambit2.db.cache
ambit2.db.chemrelation
ambit2.db.facets.datasets
ambit2.db.processors
ambit2.db.processors.quality
ambit2.db.readers
ambit2.db.reporters
ambit2.db.reporters.xlsx
ambit2.db.results
ambit2.db.search
ambit2.db.search.property
ambit2.db.search.qlabel
ambit2.db.search.structure
ambit2.db.search.structure.pairwise
ambit2.db.simiparity.space
ambit2.db.substance.ids
ambit2.db.substance.processor
ambit2.db.substance.properties
ambit2.db.substance.relation
ambit2.db.update.bundle.chemicals
ambit2.db.update.bundle.substance
ambit2.db.update.chemical
ambit2.db.update.dataset
ambit2.db.update.fpae
ambit2.db.update.qlabel
ambit2.db.update.qlabel.smarts
ambit2.db.update.storedquery
ambit2.db.update.structure
ambit2.dbui
ambit2.descriptors.processors
ambit2.namestructure
ambit2.pubchem
ambit2.pubchem.rest
ambit2.rendering
ambit2.rest.dataset
ambit2.rest.model.builder
ambit2.rest.model.predictor
ambit2.rest.model.task
ambit2.rest.rdf
ambit2.rest.rdf.chembl
ambit2.rest.rdf.sparql
ambit2.rest.structure
ambit2.rest.task.weka
ambit2.sln.io
ambit2.ui.table
ambit2.vega

Uses of IStructureRecord in ambit2.base.data

Classes in ambit2.base.data that implement IStructureRecord

Modifier and Type	Class and Description
class	StructureRecord
class	SubstanceRecord Same as the parent class, but with related structures

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

Modifier and Type	Method and Description
IStructureRelation	SubstanceRecord.addStructureRelation(String compositionUUID, IStructureRecord record, STRUCTURE_RELATION relation, Proportion value)

Uses of IStructureRecord in ambit2.base.data.study

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

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

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

Modifier and Type	Method and Description
IStructureRecord	StructureRecordValidator.process(IStructureRecord record)

Uses of IStructureRecord in ambit2.base.interfaces

Classes in ambit2.base.interfaces with type parameters of type IStructureRecord

Modifier and Type	Interface and Description
interface	IStructureRelation<RELATION_TYPE,RELATION_METRIC,FIRSTSTRUC extends IStructureRecord,SECONDSTRUC extends IStructureRecord>
interface	IStructureRelation<RELATION_TYPE,RELATION_METRIC,FIRSTSTRUC extends IStructureRecord,SECONDSTRUC extends IStructureRecord>

Uses of IStructureRecord in ambit2.base.processors

Fields in ambit2.base.processors with type parameters of type IStructureRecord

Modifier and Type	Field and Description
protected List<IStructureRecord>	StructureRecordsAppender.records

Methods in ambit2.base.processors that return types with arguments of type IStructureRecord

Modifier and Type	Method and Description
List<IStructureRecord>	StructureRecordsAppender.getRecords()
List<IStructureRecord>	StructureRecordsAppender.process(IStructureRecord target)

Methods in ambit2.base.processors with parameters of type IStructureRecord

Modifier and Type	Method and Description
List<IStructureRecord>	StructureRecordsAppender.process(IStructureRecord target)

Method parameters in ambit2.base.processors with type arguments of type IStructureRecord

Modifier and Type	Method and Description
void	StructureRecordsAppender.setRecords(List<IStructureRecord> records)

Uses of IStructureRecord in ambit2.base.processors.search

Methods in ambit2.base.processors.search that return IStructureRecord

Modifier and Type	Method and Description
IStructureRecord	AbstractFinder.process(IStructureRecord target)
protected IStructureRecord	AbstractFinder.transform(IStructureRecord record, RESULT result)
protected IStructureRecord	AbstractFinder.transformResult(IStructureRecord record, IStructureRecord result)
protected IStructureRecord	AbstractFinder.transformResult(IStructureRecord record, String result)

Methods in ambit2.base.processors.search with parameters of type IStructureRecord

Modifier and Type	Method and Description
IStructureRecord	AbstractFinder.process(IStructureRecord target)
protected Object	AbstractFinder.retrieveValue(IStructureRecord target, Property key)
protected IStructureRecord	AbstractFinder.transform(IStructureRecord record, RESULT result)
protected IStructureRecord	AbstractFinder.transformResult(IStructureRecord record, IStructureRecord result)
protected IStructureRecord	AbstractFinder.transformResult(IStructureRecord record, String result)

Uses of IStructureRecord in ambit2.base.relation

Classes in ambit2.base.relation with type parameters of type IStructureRecord

Modifier and Type	Class and Description
class	AbstractRelation<RELATION_TYPE,RELATION_METRIC extends Serializable,FIRSTSTRUC extends IStructureRecord,SECONDSTRUC extends IStructureRecord> Abstract class to represent relationship between compounds
class	AbstractRelation<RELATION_TYPE,RELATION_METRIC extends Serializable,FIRSTSTRUC extends IStructureRecord,SECONDSTRUC extends IStructureRecord> Abstract class to represent relationship between compounds

Constructors in ambit2.base.relation with parameters of type IStructureRecord

Constructor and Description
SimilarityRelation(IStructureRecord structure1, IStructureRecord structure2)
SimilarityRelation(IStructureRecord structure1, IStructureRecord structure2, Double relation)
StructureRelation(IStructureRecord structure1, IStructureRecord structure2, Double relation)
TautomerRelation(IStructureRecord structure1, IStructureRecord structure2)
TautomerRelation(IStructureRecord structure1, IStructureRecord structure2, Double relation)

Uses of IStructureRecord in ambit2.base.relation.composition

Classes in ambit2.base.relation.composition that implement IStructureRecord

Modifier and Type	Class and Description
class	Additive Substance composition: additives
class	CompositionRelation Substance composition
class	Constituent
class	Impurity Substance composition: impurities

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

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 IStructureRecord in ambit2.chebi

Fields in ambit2.chebi declared as IStructureRecord

Modifier and Type	Field and Description
protected IStructureRecord	ChEBIClient.structure

Methods in ambit2.chebi that return IStructureRecord

Modifier and Type	Method and Description
IStructureRecord	ChEBIClient.entry2structurerecord(uk.ac.ebi.chebi.webapps.chebiWS.model.LiteEntity chebiEntity, IStructureRecord struc)
IStructureRecord	ChEBIClient.next()
protected IStructureRecord	ChebiFinder.query(String term)

Methods in ambit2.chebi with parameters of type IStructureRecord

Modifier and Type	Method and Description
IStructureRecord	ChEBIClient.entry2structurerecord(uk.ac.ebi.chebi.webapps.chebiWS.model.LiteEntity chebiEntity, IStructureRecord struc)

Uses of IStructureRecord in ambit2.core.io

Fields in ambit2.core.io declared as IStructureRecord

Modifier and Type	Field and Description
protected IStructureRecord	RawIteratingWrapper.r
protected IStructureRecord	ECHAPreregistrationListReader.record
protected IStructureRecord	I5ReaderSimple.record
protected IStructureRecord	ToXMLReaderSimple.record
protected IStructureRecord	RawIteratingCSVReader.structureRecord

Methods in ambit2.core.io that return IStructureRecord

Modifier and Type	Method and Description
protected IStructureRecord	RawIteratingWrapper.createStructureRecord()
IStructureRecord	ECHAPreregistrationListReader.nextRecord()
IStructureRecord	I5ReaderSimple.nextRecord()
IStructureRecord	RawIteratingCSVReader.nextRecord()
IStructureRecord	RawIteratingFolderReader.nextRecord()
IStructureRecord	RawIteratingMOLReader.nextRecord()
IStructureRecord	RawIteratingSDFReader.nextRecord()
IStructureRecord	RawIteratingWrapper.nextRecord()
IStructureRecord	ToXMLReaderSimple.nextRecord()
protected IStructureRecord	RawIteratingCSVReader.transform(org.apache.commons.csv.CSVRecord record)

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

Modifier and Type	Method and Description
protected IRawReader<IStructureRecord>	RawIteratingFolderReader.getItemReader(int index)
static IRawReader<IStructureRecord>	FileInputState.getRawReader(InputStream stream, String extension, org.openscience.cdk.io.formats.IChemFormat format)

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

Modifier and Type	Method and Description
protected void	RawIteratingFolderReader.assignCASRN(IStructureRecord record)
protected void	RawIteratingFolderReader.assignEINECS(IStructureRecord record)
protected void	RawIteratingFolderReader.assignName(IStructureRecord record)

Uses of IStructureRecord in ambit2.core.io.dx

Methods in ambit2.core.io.dx that return IStructureRecord

Modifier and Type	Method and Description
IStructureRecord	DXParser.process(IStructureRecord record)

Methods in ambit2.core.io.dx with parameters of type IStructureRecord

Modifier and Type	Method and Description
static boolean	DXParser.hasDxProperties(IStructureRecord record)
IStructureRecord	DXParser.process(IStructureRecord record)
int	DXParser.verifySuperEndpoints(IStructureRecord record, Property p)

Uses of IStructureRecord in ambit2.core.io.json

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

Modifier and Type	Method and Description
IStructureRecord	SubstanceStudyParser.nextRecord()

Uses of IStructureRecord in ambit2.core.io.pdb

Methods in ambit2.core.io.pdb that return IStructureRecord

Modifier and Type	Method and Description
IStructureRecord	RawIteratingPDBReader.nextRecord()

Uses of IStructureRecord in ambit2.core.processors

Methods in ambit2.core.processors that return IStructureRecord

Modifier and Type	Method and Description
IStructureRecord	StructureNormalizer.process(IStructureRecord structure)

Methods in ambit2.core.processors with parameters of type IStructureRecord

Modifier and Type	Method and Description
IStructureRecord	StructureNormalizer.process(IStructureRecord structure)

Uses of IStructureRecord in ambit2.core.processors.structure

Methods in ambit2.core.processors.structure that return IStructureRecord

Modifier and Type	Method and Description
IStructureRecord	AbstractPropertyGenerator.process(IStructureRecord target)
IStructureRecord[]	MoleculePairProcessor.process(IStructureRecord[] target)
abstract IStructureRecord[]	MoleculePairProcessor.process(IStructureRecord[] target, org.openscience.cdk.interfaces.IAtomContainer[] molecules)

Methods in ambit2.core.processors.structure with parameters of type IStructureRecord

Modifier and Type	Method and Description
protected org.openscience.cdk.interfaces.IAtomContainer	AbstractPropertyGenerator.getAtomContainer(IStructureRecord target)
protected org.openscience.cdk.interfaces.IAtomContainer	MoleculeReader.handleFormat(IStructureRecord.MOL_TYPE format, IStructureRecord target)
IStructureRecord	AbstractPropertyGenerator.process(IStructureRecord target)
org.openscience.cdk.interfaces.IAtomContainer	MoleculeReader.process(IStructureRecord target)
IStructureRecord[]	MoleculePairProcessor.process(IStructureRecord[] target)
abstract IStructureRecord[]	MoleculePairProcessor.process(IStructureRecord[] target, org.openscience.cdk.interfaces.IAtomContainer[] molecules)

Uses of IStructureRecord in ambit2.core.processors.structure.key

Methods in ambit2.core.processors.structure.key with parameters of type IStructureRecord

Modifier and Type	Method and Description
protected Result	PropertyKey.getProperty(IStructureRecord structure)
String	CASKey.process(IStructureRecord structure)
String	ChEMBLCompoundURI.process(IStructureRecord structure)
Number	DSSToxID.process(IStructureRecord structure)
String	EINECSKey.process(IStructureRecord structure)
Result	PropertyKey.process(IStructureRecord structure)
String	PropertyNameKey.process(IStructureRecord structure)
Number	PubchemCID.process(IStructureRecord structure)
Number	PubchemSID.process(IStructureRecord structure)
String	ReferenceSubstanceUUID.process(IStructureRecord structure)

Uses of IStructureRecord in ambit2.db

Methods in ambit2.db with parameters of type IStructureRecord

Modifier and Type	Method and Description
protected void	DbReaderStructure.cache(String category, String key, IStructureRecord object, boolean ok)
protected DbReader.cached_results	DbReaderStructure.getCached(String category, String key, IStructureRecord object)
protected boolean	DbReaderStructure.prescreen(net.idea.modbcum.i.IQueryRetrieval<IStructureRecord> query, IStructureRecord object)

Method parameters in ambit2.db with type arguments of type IStructureRecord

Modifier and Type	Method and Description
protected boolean	DbReaderStructure.prescreen(net.idea.modbcum.i.IQueryRetrieval<IStructureRecord> query, IStructureRecord object)

Uses of IStructureRecord in ambit2.db.cache

Methods in ambit2.db.cache that return IStructureRecord

Modifier and Type	Method and Description
IStructureRecord	RetrieveStructureImagePath.getObject(ResultSet rs)

Constructors in ambit2.db.cache with parameters of type IStructureRecord

Constructor and Description
QueryCachedResults(String category, String key, IStructureRecord record)
QueryCachedResultsBoolean(String category, String key, IStructureRecord record)
RetrieveStructureImagePath(String mimeType, IStructureRecord record)

Uses of IStructureRecord in ambit2.db.chemrelation

Classes in ambit2.db.chemrelation with type parameters of type IStructureRecord

Modifier and Type	Class and Description
class	AbstractUpdateStructureRelation<S extends IStructureRecord,O extends IStructureRecord,RELATION,METRIC>
class	AbstractUpdateStructureRelation<S extends IStructureRecord,O extends IStructureRecord,RELATION,METRIC>

Methods in ambit2.db.chemrelation with parameters of type IStructureRecord

Modifier and Type	Method and Description
double	ReadStructureRelation.calculateMetric(IStructureRecord object)
protected void	ReadStructureRelation.retrieveMetric(IStructureRecord record, ResultSet rs)

Constructors in ambit2.db.chemrelation with parameters of type IStructureRecord

Constructor and Description
DeleteStructureRelation(IStructureRecord structure1, IStructureRecord structure2, String relation)
ReadStructureRelation(IStructureRecord structure)
UpdateStructureRelation(IStructureRecord structure1, IStructureRecord structure2, String relation)
UpdateStructureRelation(IStructureRecord structure1, IStructureRecord structure2, String relation, Double metric)

Uses of IStructureRecord in ambit2.db.facets.datasets

Fields in ambit2.db.facets.datasets declared as IStructureRecord

Modifier and Type	Field and Description
protected IStructureRecord	DatasetPrefixFacet.structure

Methods in ambit2.db.facets.datasets that return IStructureRecord

Modifier and Type	Method and Description
IStructureRecord	DatasetPrefixFacet.getStructure()

Methods in ambit2.db.facets.datasets with parameters of type IStructureRecord

Modifier and Type	Method and Description
void	DatasetByPrefixNameFacetQuery.setFieldname(IStructureRecord fieldname)
void	DatasetPrefixFacet.setStructure(IStructureRecord structure)

Uses of IStructureRecord in ambit2.db.processors

Fields in ambit2.db.processors declared as IStructureRecord

Modifier and Type	Field and Description
protected IStructureRecord	ValueWriter.structure

Fields in ambit2.db.processors with type parameters of type IStructureRecord

Modifier and Type	Field and Description
protected QueryExecutor<net.idea.modbcum.i.IQueryObject<IStructureRecord>>	ProcessorStructureRetrieval.exec
protected net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>	ProcessorSetQueryScope.query
protected net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>	ProcessorStructureRetrieval.query

Methods in ambit2.db.processors that return IStructureRecord

Modifier and Type	Method and Description
IStructureRecord	ValueWriter.getStructure()
IStructureRecord	DescriptorsCalculator.process(IStructureRecord target)
IStructureRecord	ProcessorStructureRetrieval.process(IStructureRecord target)
protected IStructureRecord	ProcessorStructureRetrieval.selectResult(IStructureRecord target, ResultSet rs)
protected IStructureRecord	PropertyValuesWriter.transform(IStructureRecord target)
IStructureRecord	DbStructureWriter.update(IStructureRecord structure)
IStructureRecord	DbStructureWriter.write(IStructureRecord structure)
IStructureRecord	FP1024Writer.write(IStructureRecord record)
IStructureRecord	PropertyValuesWriter.write(IStructureRecord target)
IStructureRecord	ValueWriterNew.write(IStructureRecord recordToStore)

Methods in ambit2.db.processors that return types with arguments of type IStructureRecord

Modifier and Type	Method and Description
List<IStructureRecord>	RepositoryWriter.create(IStructureRecord arg0)
Iterator<IStructureRecord>	BatchStructuresListProcessor.getIterator(List<IStructureRecord> target)
net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>	ProcessorSetQueryScope.getQuery()
net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>	ProcessorStructureRetrieval.getQuery()
net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>	ProcessorSetQueryScope.process(net.idea.modbcum.i.IQueryRetrieval<IStructureRecord> target)
net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>	ProcessorCreateProfileQuery.process(Profile<Property> target)
List<IStructureRecord>	RepositoryWriter.update(IStructureRecord arg0)
List<IStructureRecord>	PropertyImporter.write(org.openscience.cdk.interfaces.IAtomContainer molecule)
List<IStructureRecord>	RepositoryWriter.write(IStructureRecord structure)
List<IStructureRecord>	DbStructureWriter.writeStructure(IStructureRecord structure, boolean update)

Methods in ambit2.db.processors with parameters of type IStructureRecord

Modifier and Type	Method and Description
List<IStructureRecord>	RepositoryWriter.create(IStructureRecord arg0)
protected void	RepositoryWriter.findChemical(IStructureRecord record)
protected String	PropertyValuesWriter.getComments(String name, IStructureRecord target)
protected Iterable<Property>	PropertyValuesWriter.getPropertyNames(IStructureRecord record)
protected AbstractStructureQuery	RepositoryWriter.getQuery(IStructureRecord record)
protected String[]	StructureStatisticsProcessor.getSQL(IStructureRecord target)
protected Object	PropertyValuesWriter.getValue(IStructureRecord record, Property property, int index)
protected void	ValueWriterNew.prepareBatchProperties(IStructureRecord record, Connection connection)
protected void	ValueWriterNew.prepareBatchValues(IStructureRecord record, Connection connection)
protected void	ValueWriterNew.prepareStatementValues(IStructureRecord record, Property property)
abstract INTERNAL	AbstractDescriptorCalculator.preprocess(IStructureRecord target)
org.openscience.cdk.interfaces.IAtomContainer	DescriptorsCalculator.preprocess(IStructureRecord target)
IStructureRecord	DescriptorsCalculator.process(IStructureRecord target)
IStructureRecord	ProcessorStructureRetrieval.process(IStructureRecord target)
StringBuffer	StructureStatisticsProcessor.process(IStructureRecord target)
protected void	ValueWriterNew.retrieveProperties(IStructureRecord record)
protected IStructureRecord	ProcessorStructureRetrieval.selectResult(IStructureRecord target, ResultSet rs)
void	ValueWriter.setStructure(IStructureRecord structure)
protected IStructureRecord	PropertyValuesWriter.transform(IStructureRecord target)
IStructureRecord	DbStructureWriter.update(IStructureRecord structure)
List<IStructureRecord>	RepositoryWriter.update(IStructureRecord arg0)
IStructureRecord	DbStructureWriter.write(IStructureRecord structure)
IStructureRecord	FP1024Writer.write(IStructureRecord record)
IStructureRecord	PropertyValuesWriter.write(IStructureRecord target)
List<IStructureRecord>	RepositoryWriter.write(IStructureRecord structure)
IStructureRecord	ValueWriterNew.write(IStructureRecord recordToStore)
protected void	DbStructureWriter.writeDataset(IStructureRecord structure)
protected void	PropertyImporter.writeDataset(IStructureRecord structure)
void	DbStructureWriter.writeProperties(IStructureRecord structure)
List<IStructureRecord>	DbStructureWriter.writeStructure(IStructureRecord structure, boolean update)

Method parameters in ambit2.db.processors with type arguments of type IStructureRecord

Modifier and Type	Method and Description
Iterator<IStructureRecord>	BatchStructuresListProcessor.getIterator(List<IStructureRecord> target)
protected int	ProcessorCreateQuery.insertScreenedResults(IStoredQuery result, net.idea.modbcum.i.IQueryRetrieval<IStructureRecord> query)
IStoredQuery	ProcessorCreateQuery.process(net.idea.modbcum.i.IQueryObject<IStructureRecord> target)
net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>	ProcessorSetQueryScope.process(net.idea.modbcum.i.IQueryRetrieval<IStructureRecord> target)
void	ProcessorSetQueryScope.setQuery(net.idea.modbcum.i.IQueryRetrieval<IStructureRecord> query)
void	ProcessorStructureRetrieval.setQuery(net.idea.modbcum.i.IQueryRetrieval<IStructureRecord> query)

Constructor parameters in ambit2.db.processors with type arguments of type IStructureRecord

Constructor and Description
ProcessorStructureRetrieval(net.idea.modbcum.i.IQueryRetrieval<IStructureRecord> query)

Uses of IStructureRecord in ambit2.db.processors.quality

Methods in ambit2.db.processors.quality that return IStructureRecord

Modifier and Type	Method and Description
IStructureRecord	QualityLabelWriter.create(IStructureRecord record)

Methods in ambit2.db.processors.quality with parameters of type IStructureRecord

Modifier and Type	Method and Description
BitSet	FPStructureWriter.create(IStructureRecord record)
IStructureRecord	QualityLabelWriter.create(IStructureRecord record)
Property	QualityValueWriter.create(IStructureRecord record)

Uses of IStructureRecord in ambit2.db.readers

Fields in ambit2.db.readers declared as IStructureRecord

Modifier and Type	Field and Description
protected IStructureRecord	RetrieveGroupedValuesByAlias.record
protected IStructureRecord	RetrieveProfileValues.record
protected IStructureRecord	RetrieveProfileValuesAsRow.record
protected IStructureRecord	RetrieveTemplateStructure.record

Methods in ambit2.db.readers that return IStructureRecord

Modifier and Type	Method and Description
IStructureRecord	RetrieveProfileValues.getMultiObject(ResultSet rs)
IStructureRecord	ReadChemicalIds.getObject(ResultSet rs)
IStructureRecord	RetrieveFieldStructure.getObject(ResultSet rs)
IStructureRecord	RetrieveGroupedValuesByAlias.getObject(ResultSet rs)
IStructureRecord	RetrieveProfileValues.getObject(ResultSet rs)
IStructureRecord	RetrieveProfileValuesAsRow.getObject(ResultSet rs)
IStructureRecord	RetrieveStructure.getObject(ResultSet rs)
IStructureRecord	RetrieveTemplateStructure.getObject(ResultSet rs)
protected IStructureRecord	RetrieveProfileValues.getObject(ResultSet rs, IStructureRecord record, int idstructure)
IStructureRecord	RetrieveGroupedValuesByAlias.getRecord()
IStructureRecord	RetrieveProfileValues.getRecord()
IStructureRecord	RetrieveProfileValuesAsRow.getRecord()
IStructureRecord	RetrieveTemplateStructure.getRecord()

Methods in ambit2.db.readers with parameters of type IStructureRecord

Modifier and Type	Method and Description
double	ReadChemicalIds.calculateMetric(IStructureRecord object)
double	RetrieveGroupedValuesByAlias.calculateMetric(IStructureRecord object)
double	RetrieveProfileValues.calculateMetric(IStructureRecord object)
double	RetrieveProfileValuesAsRow.calculateMetric(IStructureRecord object)
protected abstract Result	ValuesByTemplateReader.createResult(IStructureRecord target)
protected IStructureRecord	RetrieveProfileValues.getObject(ResultSet rs, IStructureRecord record, int idstructure)
Result	ValuesByTemplateReader.process(IStructureRecord target)
protected void	RetrieveProfileValues.retrieveValue(ResultSet rs, IStructureRecord record, Property p)
void	RetrieveGroupedValuesByAlias.setRecord(IStructureRecord record)
void	RetrieveProfileValues.setRecord(IStructureRecord record)
void	RetrieveProfileValuesAsRow.setRecord(IStructureRecord record)
void	RetrieveTemplateStructure.setRecord(IStructureRecord record)
void	RetrieveAtomContainer.setValue(IStructureRecord value)
void	RetrieveStructure.setValue(IStructureRecord value)

Constructors in ambit2.db.readers with parameters of type IStructureRecord

Constructor and Description
RetrieveDatasets(IStructureRecord record, SourceDataset dataset)

Uses of IStructureRecord in ambit2.db.reporters

Classes in ambit2.db.reporters with type parameters of type IStructureRecord

Modifier and Type	Class and Description
class	AbstractImageReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,OUTPUT>
class	ARFF3ColReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>>
class	ARFFReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>>
class	CMLReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> Writes query results as CML .
class	CSVReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>>
class	ImageAreaReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>>
class	ImageReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> SELECT idchemical,idstructure,text,title FROM structure left join query_results using(idchemical,idstructure) left join `query` using(idquery) left join sessions using(idsessions) where sessions.title="SMARTS" and idchemical=460 and idstructure=100664 union SELECT idchemical,idstructure,null,"SMARTS" FROM structure where idchemical=460 and idstructure=100664
class	PDFReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> Generates PDF
class	QueryHeaderReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,Output> Generates report from a query with header at a top (e.g.
class	QueryPacketReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,Output>
class	QueryStructureReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,Output> Parent class for all reporters working with structure queries.
class	RTFReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>>
class	SDFReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>>
class	SmilesReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>>

Methods in ambit2.db.reporters that return types with arguments of type IStructureRecord

Modifier and Type	Method and Description
protected net.idea.modbcum.p.batch.AbstractBatchProcessor<net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,IStructureRecord>	QueryStructureReporter.createBatch(Q query)
protected net.idea.modbcum.p.batch.AbstractBatchProcessor<net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,IStructureRecord>	QueryStructureReporter.createBatch(Q query)

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

Modifier and Type	Method and Description
protected String	AbstractImageReporter.cache(IStructureRecord item, BufferedImage image)
protected CachedImage<OUTPUT>	AbstractImageReporter.createImage(IStructureRecord item)
protected abstract CachedImage<OUTPUT>	AbstractImageReporter.getCached(IStructureRecord item)
protected CachedImage<StringWriter>	ImageAreaReporter.getCached(IStructureRecord item)
protected CachedImage<BufferedImage>	ImageReporter.getCached(IStructureRecord item)
protected File	AbstractImageReporter.getFilePath(String tmpDir, String dbName, String dimensions, IStructureRecord item, String ext)
protected String	SDFReporter.getSDFContent(IStructureRecord item)
protected String	CSVReporter.getURI(IStructureRecord item)
Object	AbstractImageReporter.processItem(IStructureRecord item)
Object	ARFF3ColReporter.processItem(IStructureRecord item)
Object	ARFFReporter.processItem(IStructureRecord item)
Object	CMLReporter.processItem(IStructureRecord item)
Object	CSVReporter.processItem(IStructureRecord item)
Object	ImageAreaReporter.processItem(IStructureRecord item)
Object	SDFReporter.processItem(IStructureRecord item)
Object	SmilesReporter.processItem(IStructureRecord item)
Object	StructureListReporter.processItem(IStructureRecord item)
Object	StructureRecordReporter.processItem(IStructureRecord item)
Object	PDFReporter.processItem(IStructureRecord item)
Object	RTFReporter.processItem(IStructureRecord item)

Method parameters in ambit2.db.reporters with type arguments of type IStructureRecord

Modifier and Type	Method and Description
void	AbstractStructureRecordReporter.footer(Result output, net.idea.modbcum.i.IQueryRetrieval<IStructureRecord> query)
void	AbstractStructureRecordReporter.header(Result output, net.idea.modbcum.i.IQueryRetrieval<IStructureRecord> query)

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

Constructor and Description
StructureRecordReporter(IStructureRecord record, Profile groupedProperties, Template template)

Constructor parameters in ambit2.db.reporters with type arguments of type IStructureRecord

Constructor and Description
StructureListReporter(List<IStructureRecord> record, Profile groupedProperties, Template template)

Uses of IStructureRecord in ambit2.db.reporters.xlsx

Classes in ambit2.db.reporters.xlsx with type parameters of type IStructureRecord

Modifier and Type	Class and Description
class	AbstractXLSXReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>>
class	StructureRecordXLSXReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>>
class	SubstanceRecordXLSXReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>>

Methods in ambit2.db.reporters.xlsx with parameters of type IStructureRecord

Modifier and Type	Method and Description
protected void	StructureRecordXLSXReporter.addPicture(IStructureRecord record, int row, int column)
Object	StructureRecordXLSXReporter.processItem(IStructureRecord item)
Object	SubstanceRecordXLSXReporter.processItem(IStructureRecord item)

Uses of IStructureRecord in ambit2.db.results

Methods in ambit2.db.results that return IStructureRecord

Modifier and Type	Method and Description
IStructureRecord	StoredQueryTableModel.getRecord(int rowIndex, int columnIndex)

Methods in ambit2.db.results with parameters of type IStructureRecord

Modifier and Type	Method and Description
org.openscience.cdk.interfaces.IAtomContainer	StoredQueryTableModel.getAtomContainer(IStructureRecord record)
protected Object	StoredQueryTableModel.getField(IStructureRecord record, Property fieldname)
protected String	StoredQueryTableModel.getLabel(IStructureRecord record, int offset)
String	StoredQueryTableModel.getStatsAt(IStructureRecord record)
protected void	StoredQueryTableModel.selectRecords(IStructureRecord record, boolean value)
void	StoredQueryTableModel.update(int record, IStructureRecord struc)

Uses of IStructureRecord in ambit2.db.search

Fields in ambit2.db.search declared as IStructureRecord

Modifier and Type	Field and Description
protected IStructureRecord	QuerySmilesByID.maxValue

Fields in ambit2.db.search with type parameters of type IStructureRecord

Modifier and Type	Field and Description
protected net.idea.modbcum.i.IQueryObject<IStructureRecord>	StoredQuery.query

Methods in ambit2.db.search that return IStructureRecord

Modifier and Type	Method and Description
IStructureRecord	QuerySmilesByID.getMaxValue()
IStructureRecord	QuerySmilesByID.getObject(ResultSet rs)

Methods in ambit2.db.search that return types with arguments of type IStructureRecord

Modifier and Type	Method and Description
net.idea.modbcum.i.IQueryObject<IStructureRecord>	IStoredQuery.getQuery()
net.idea.modbcum.i.IQueryObject<IStructureRecord>	StoredQuery.getQuery()

Methods in ambit2.db.search with parameters of type IStructureRecord

Modifier and Type	Method and Description
double	QuerySmilesByID.calculateMetric(IStructureRecord object)
void	QuerySmilesByID.setMaxValue(IStructureRecord maxValue)

Method parameters in ambit2.db.search with type arguments of type IStructureRecord

Modifier and Type	Method and Description
void	IStoredQuery.setQuery(net.idea.modbcum.i.IQueryObject<IStructureRecord> query)
void	StoredQuery.setQuery(net.idea.modbcum.i.IQueryObject<IStructureRecord> query)

Constructors in ambit2.db.search with parameters of type IStructureRecord

Constructor and Description
QuerySmilesByID(IStructureRecord record)

Uses of IStructureRecord in ambit2.db.search.property

Methods in ambit2.db.search.property that return IStructureRecord

Modifier and Type	Method and Description
protected IStructureRecord	ValuesReader.createResult(IStructureRecord target)
IStructureRecord	ValuesReader.process(IStructureRecord target)

Methods in ambit2.db.search.property with parameters of type IStructureRecord

Modifier and Type	Method and Description
protected IStructureRecord	ValuesReader.createResult(IStructureRecord target)
IStructureRecord	ValuesReader.process(IStructureRecord target)
protected void	ValuesReader.set(IStructureRecord result, Property fieldname, Object value)

Uses of IStructureRecord in ambit2.db.search.qlabel

Constructors in ambit2.db.search.qlabel with parameters of type IStructureRecord

Constructor and Description
QueryConsensus(IStructureRecord record, String label)
QueryQLabel(AmbitUser user, IStructureRecord record)

Uses of IStructureRecord in ambit2.db.search.structure

Fields in ambit2.db.search.structure declared as IStructureRecord

Modifier and Type	Field and Description
protected IStructureRecord	QueryStructureByID.maxValue

Methods in ambit2.db.search.structure that return IStructureRecord

Modifier and Type	Method and Description
IStructureRecord	QueryStructureByID.getMaxValue()
IStructureRecord	AbstractStructureQuery.getObject(ResultSet rs)
IStructureRecord	ChemicalByQueryFolder.getObject(ResultSet rs)
IStructureRecord	FingerprintsByStatus.getObject(ResultSet rs)
IStructureRecord	FreeTextQuery.getObject(ResultSet rs)
IStructureRecord	QueryDataset.getObject(ResultSet rs)
IStructureRecord	QueryFieldAbstract.getObject(ResultSet rs)
IStructureRecord	QueryStructure.getObject(ResultSet rs)
IStructureRecord	ScopeQuery.getObject(ResultSet rs)

Methods in ambit2.db.search.structure that return types with arguments of type IStructureRecord

Modifier and Type	Method and Description
abstract net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>	SCOPE.createQuery()
net.idea.modbcum.i.IQueryObject<IStructureRecord>	ProcessorMissingDescriptorsQuery.process(Profile<Property> descriptors)

Methods in ambit2.db.search.structure with parameters of type IStructureRecord

Modifier and Type	Method and Description
double	AbstractStructureQuery.calculateMetric(IStructureRecord object)
double	QueryExactStructure.calculateMetric(IStructureRecord object) Deprecated.
double	QueryPrescreenBitSet.calculateMetric(IStructureRecord item)
double	QuerySimilarityBitset.calculateMetric(IStructureRecord object)
double	QuerySimilarityStructure.calculateMetric(IStructureRecord object)
double	QuerySMARTS.calculateMetric(IStructureRecord object)
double	QueryStructureByQualityPairLabel.calculateMetric(IStructureRecord object)
double	ScopeQuery.calculateMetric(IStructureRecord object)
protected void	AbstractStructureQuery.retrieveMetric(IStructureRecord record, ResultSet rs)
protected void	QuerySimilarity.retrieveMetric(IStructureRecord record, ResultSet rs)
protected void	AbstractStructureQuery.retrieveStrucType(IStructureRecord record, ResultSet rs)
protected void	QueryStrucType.retrieveStrucType(IStructureRecord record, ResultSet rs)
void	QueryStructureByID.setMaxValue(IStructureRecord maxValue)
void	QueryLookupStructure.setValue(IStructureRecord value)

Constructors in ambit2.db.search.structure with parameters of type IStructureRecord

Constructor and Description
QueryStructureByID(IStructureRecord record)

Uses of IStructureRecord in ambit2.db.search.structure.pairwise

Fields in ambit2.db.search.structure.pairwise declared as IStructureRecord

Modifier and Type	Field and Description
protected IStructureRecord[]	QueryStructurePairs.records
protected IStructureRecord[]	RetrieveStructurePair.records

Methods in ambit2.db.search.structure.pairwise that return IStructureRecord

Modifier and Type	Method and Description
IStructureRecord[]	QueryStructurePairs.getObject(ResultSet rs)
IStructureRecord[]	RetrieveStructurePair.getObject(ResultSet rs)
IStructureRecord[]	PairPropertiesWriter.process(IStructureRecord[] target)
IStructureRecord[]	ProcessorStructurePairsRetrieval.process(IStructureRecord[] target)

Methods in ambit2.db.search.structure.pairwise with parameters of type IStructureRecord

Modifier and Type	Method and Description
double	QueryStructurePairs.calculateMetric(IStructureRecord[] object)
double	RetrieveStructurePair.calculateMetric(IStructureRecord[] object)
protected void	RetrieveStructurePair.getObject(ResultSet rs, IStructureRecord r, int offset)
IStructureRecord[]	PairPropertiesWriter.process(IStructureRecord[] target)
IStructureRecord[]	ProcessorStructurePairsRetrieval.process(IStructureRecord[] target)
protected boolean	RetrieveStructurePair.retrieve(IStructureRecord record)

Uses of IStructureRecord in ambit2.db.simiparity.space

Fields in ambit2.db.simiparity.space declared as IStructureRecord

Modifier and Type	Field and Description
protected IStructureRecord	QMapSpace.record

Methods in ambit2.db.simiparity.space that return IStructureRecord

Modifier and Type	Method and Description
IStructureRecord	QMapSpace.getRecord()

Methods in ambit2.db.simiparity.space with parameters of type IStructureRecord

Modifier and Type	Method and Description
double	QueryQMapStructures.calculateMetric(IStructureRecord object)
protected void	QueryQMapStructures.retrieveMetric(IStructureRecord record, ResultSet rs)
void	QMapSpace.setRecord(IStructureRecord record)

Uses of IStructureRecord in ambit2.db.substance.ids

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

Modifier and Type	Method and Description
IStructureRecord	ReadChemIdentifiersByComposition.getObject(ResultSet rs)

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

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

Uses of IStructureRecord in ambit2.db.substance.processor

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

Modifier and Type	Method and Description
IStructureRecord	DBMatrixValueMarker.process(IStructureRecord record)
IStructureRecord	DBSubstanceWriter.process(IStructureRecord record)

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

Modifier and Type	Method and Description
IStructureRecord	DBMatrixValueMarker.process(IStructureRecord record)
IStructureRecord	DBSubstanceWriter.process(IStructureRecord record)

Uses of IStructureRecord in ambit2.db.substance.properties

Fields in ambit2.db.substance.properties declared as IStructureRecord

Modifier and Type	Field and Description
protected IStructureRecord	ReadChemPropertiesByComposition.record

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

Modifier and Type	Method and Description
IStructureRecord	ReadChemPropertiesByComposition.getObject(ResultSet rs)
IStructureRecord	ReadChemPropertiesByComposition.getRecord()

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

Modifier and Type	Method and Description
double	ReadChemPropertiesByComposition.calculateMetric(IStructureRecord object)
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!
void	ReadChemPropertiesByComposition.setRecord(IStructureRecord record)

Uses of IStructureRecord in ambit2.db.substance.relation

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

Modifier and Type	Method and Description
IStructureRecord	ChemicalBySubstanceRelation.getObject(ResultSet rs)
IStructureRecord	ReadSubstanceRelation.getObject(ResultSet rs)

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

Modifier and Type	Method and Description
double	ReadSubstanceRelation.calculateMetric(IStructureRecord object)
protected void	ReadSubstanceRelation.retrieveMetric(IStructureRecord record, ResultSet rs)

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

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

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

Methods in ambit2.db.update.bundle.chemicals that return IStructureRecord

Modifier and Type	Method and Description
IStructureRecord	ReadChemicalsByBundle.getObject(ResultSet rs)

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

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

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

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

Modifier and Type	Method and Description
void	AddCompoundAsSubstanceToBundle.setCompound(IStructureRecord compound)
static SubstanceRecord	AddCompoundAsSubstanceToBundle.structure2substance(IStructureRecord compound)

Uses of IStructureRecord in ambit2.db.update.chemical

Methods in ambit2.db.update.chemical that return IStructureRecord

Modifier and Type	Method and Description
IStructureRecord	InChIChemicalsWriter.process(IStructureRecord target)

Methods in ambit2.db.update.chemical with parameters of type IStructureRecord

Modifier and Type	Method and Description
IStructureRecord	InChIChemicalsWriter.process(IStructureRecord target)

Uses of IStructureRecord in ambit2.db.update.dataset

Fields in ambit2.db.update.dataset declared as IStructureRecord

Modifier and Type	Field and Description
protected IStructureRecord	QueryDatasetByFeatures.structure

Methods in ambit2.db.update.dataset that return IStructureRecord

Modifier and Type	Method and Description
IStructureRecord	QueryDatasetByFeatures.getStructure()

Methods in ambit2.db.update.dataset with parameters of type IStructureRecord

Modifier and Type	Method and Description
void	QueryDatasetByFeatures.setStructure(IStructureRecord structure)

Constructors in ambit2.db.update.dataset with parameters of type IStructureRecord

Constructor and Description
DatasetAddStructure(SourceDataset dataset, IStructureRecord record)
DatasetDeleteStructure(SourceDataset dataset, IStructureRecord record)

Uses of IStructureRecord in ambit2.db.update.fpae

Methods in ambit2.db.update.fpae with parameters of type IStructureRecord

Modifier and Type	Method and Description
S	AtomEnvironmentMatrixWriter.create(IStructureRecord record)
S	AtomEnvironmentWriter.create(IStructureRecord record) Deprecated.

Uses of IStructureRecord in ambit2.db.update.qlabel

Constructors in ambit2.db.update.qlabel with parameters of type IStructureRecord

Constructor and Description
CreateStructureQLabel(IStructureRecord record, QLabel label)
DeleteStructureQLabel(IStructureRecord record, QLabel label)

Uses of IStructureRecord in ambit2.db.update.qlabel.smarts

Methods in ambit2.db.update.qlabel.smarts that return IStructureRecord

Modifier and Type	Method and Description
IStructureRecord	SMARTSAcceleratorWriter.create(IStructureRecord record)

Methods in ambit2.db.update.qlabel.smarts with parameters of type IStructureRecord

Modifier and Type	Method and Description
IStructureRecord	SMARTSAcceleratorWriter.create(IStructureRecord record)

Uses of IStructureRecord in ambit2.db.update.storedquery

Constructors in ambit2.db.update.storedquery with parameters of type IStructureRecord

Constructor and Description
QueryDeleteStructure(IStoredQuery dataset, IStructureRecord record)

Uses of IStructureRecord in ambit2.db.update.structure

Methods in ambit2.db.update.structure that return IStructureRecord

Modifier and Type	Method and Description
IStructureRecord	ChemicalByDataset.getObject(ResultSet rs)

Methods in ambit2.db.update.structure with parameters of type IStructureRecord

Modifier and Type	Method and Description
void	CreateStructure.setObject(IStructureRecord object)

Constructors in ambit2.db.update.structure with parameters of type IStructureRecord

Constructor and Description
CreateStructure(IStructureRecord structure)
DeleteStructure(IStructureRecord structure)
UpdateStructure(IStructureRecord structure)

Uses of IStructureRecord in ambit2.dbui

Method parameters in ambit2.dbui with type arguments of type IStructureRecord

Modifier and Type	Method and Description
protected void	QueryCombinedEditor.setScope(net.idea.modbcum.i.IQueryRetrieval<IStructureRecord> scopeQuery)

Uses of IStructureRecord in ambit2.descriptors.processors

Fields in ambit2.descriptors.processors declared as IStructureRecord

Modifier and Type	Field and Description
protected IStructureRecord	DescriptorValue2Property.structure

Methods in ambit2.descriptors.processors that return IStructureRecord

Modifier and Type	Method and Description
IStructureRecord	DescriptorValue2Property.getStructure()
IStructureRecord	DescriptorValue2Property.process(org.openscience.cdk.qsar.DescriptorValue descriptor)

Methods in ambit2.descriptors.processors with parameters of type IStructureRecord

Modifier and Type	Method and Description
protected org.openscience.cdk.interfaces.IAtomContainer	BitSetGenerator.getAtomContainer(IStructureRecord target)
void	DescriptorValue2Property.setStructure(IStructureRecord structure)

Uses of IStructureRecord in ambit2.namestructure

Fields in ambit2.namestructure declared as IStructureRecord

Modifier and Type	Field and Description
protected IStructureRecord	Name2StructureFinder.record

Methods in ambit2.namestructure that return IStructureRecord

Modifier and Type	Method and Description
protected IStructureRecord	Name2StructureFinder.query(String value)

Uses of IStructureRecord in ambit2.pubchem

Fields in ambit2.pubchem with type parameters of type IStructureRecord

Modifier and Type	Field and Description
protected QuerySupport<List<IStructureRecord>,List<IStructureRecord>>	PUGProcessor.support
protected QuerySupport<List<IStructureRecord>,List<IStructureRecord>>	PUGProcessor.support

Methods in ambit2.pubchem that return IStructureRecord

Modifier and Type	Method and Description
protected IStructureRecord	PubchemFinder.query(String term)

Methods in ambit2.pubchem that return types with arguments of type IStructureRecord

Modifier and Type	Method and Description
protected HTTPRequest<List<IStructureRecord>,List<IStructureRecord>>	PUGProcessor.createDownloadHTTPRequest(List<IStructureRecord> record)
protected HTTPRequest<List<IStructureRecord>,List<IStructureRecord>>	PUGProcessor.createDownloadHTTPRequest(List<IStructureRecord> record)
protected HTTPRequest<List<IStructureRecord>,List<IStructureRecord>>	PUGProcessor.createPollRequest(List<IStructureRecord> waitingregids)
protected HTTPRequest<List<IStructureRecord>,List<IStructureRecord>>	PUGProcessor.createPollRequest(List<IStructureRecord> waitingregids)
protected List<IStructureRecord>	EntrezESearchParser.parse(Document doc)
protected List<IStructureRecord>	EntrezSearchProcessor.parseInput(String target, InputStream in)
static List<IStructureRecord>	PUGProcessor.parseOutput(Document doc)
List<IStructureRecord>	EntrezESearchParser.process(InputStream target)
List<IStructureRecord>	PUGProcessor.process(List<IStructureRecord> target) Example: You want to download CID 1 and CID 99 being uids 1 and 99 in the 'pccompound' Entrez database in SDF format with gzip compression.
List<IStructureRecord>	EntrezSearchProcessor.process(String target)
protected static List<IStructureRecord>	PUGProcessor.processDownloadURL(Document doc, Element download)
protected static List<IStructureRecord>	PUGProcessor.processWaiting(Document doc, Element waiting)

Methods in ambit2.pubchem with parameters of type IStructureRecord

Modifier and Type	Method and Description
static void	PUGProcessor.createPollRequest(IStructureRecord regid, Writer out)
protected String	EntrezSearchProcessor.format(IStructureRecord record, String source, String einecs)

Method parameters in ambit2.pubchem with type arguments of type IStructureRecord

Modifier and Type	Method and Description
protected HTTPRequest<List<IStructureRecord>,List<IStructureRecord>>	PUGProcessor.createDownloadHTTPRequest(List<IStructureRecord> record)
void	PUGProcessor.createDownloadRequest(List<IStructureRecord> sids, Writer out)
protected HTTPRequest<List<IStructureRecord>,List<IStructureRecord>>	PUGProcessor.createPollRequest(List<IStructureRecord> waitingregids)
List<IStructureRecord>	PUGProcessor.process(List<IStructureRecord> target) Example: You want to download CID 1 and CID 99 being uids 1 and 99 in the 'pccompound' Entrez database in SDF format with gzip compression.

Uses of IStructureRecord in ambit2.pubchem.rest

Methods in ambit2.pubchem.rest that return IStructureRecord

Modifier and Type	Method and Description
protected IStructureRecord	PubChemRestFinder.query(String term)

Methods in ambit2.pubchem.rest that return types with arguments of type IStructureRecord

Modifier and Type	Method and Description
protected List<IStructureRecord>	PUGRestCompoundRequest.read(InputStream in)

Methods in ambit2.pubchem.rest with parameters of type IStructureRecord

Modifier and Type	Method and Description
protected Object	PubChemRestFinder.retrieveValue(IStructureRecord target, Property key)

Uses of IStructureRecord in ambit2.rendering

Methods in ambit2.rendering with parameters of type IStructureRecord

Modifier and Type	Method and Description
String	StructureEditorProcessor.process(IStructureRecord record)

Uses of IStructureRecord in ambit2.rest.dataset

Classes in ambit2.rest.dataset with type parameters of type IStructureRecord

Modifier and Type	Class and Description
class	DatasetRDFStaxReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>>

Fields in ambit2.rest.dataset with type parameters of type IStructureRecord

Modifier and Type	Field and Description
protected CompoundURIReporter<net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>>	DatasetRDFWriter.compoundReporter

Methods in ambit2.rest.dataset that return IStructureRecord

Modifier and Type	Method and Description
IStructureRecord	DatasetRDFWriter.process(IStructureRecord item)
IStructureRecord	RDFFileWriter.process(IStructureRecord target)

Methods in ambit2.rest.dataset that return types with arguments of type IStructureRecord

Modifier and Type	Method and Description
protected net.idea.modbcum.p.batch.AbstractBatchProcessor<net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,IStructureRecord>	DatasetRDFStaxReporter.createBatch(Q query)
protected net.idea.modbcum.p.batch.AbstractBatchProcessor<net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,IStructureRecord>	DatasetRDFStaxReporter.createBatch(Q query)
protected RDFObjectIterator<IStructureRecord>	RDFStructuresReader.createObjectIterator(org.restlet.data.Reference target, org.restlet.data.MediaType mediaType)
protected net.idea.restnet.db.QueryURIReporter<IStructureRecord,net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>>	DatasetRDFStaxReporter.createURIReporter(org.restlet.Request req, net.idea.restnet.c.ResourceDoc doc)
protected net.idea.restnet.db.QueryURIReporter<IStructureRecord,net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>>	DatasetRDFStaxReporter.createURIReporter(org.restlet.Request req, net.idea.restnet.c.ResourceDoc doc)
CompoundURIReporter<net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>>	DatasetRDFWriter.getCompoundReporter()

Methods in ambit2.rest.dataset with parameters of type IStructureRecord

Modifier and Type	Method and Description
IStructureRecord	DatasetRDFWriter.process(IStructureRecord item)
IStructureRecord	RDFFileWriter.process(IStructureRecord target)
Object	DatasetRDFStaxReporter.processItem(IStructureRecord item)

Method parameters in ambit2.rest.dataset with type arguments of type IStructureRecord

Modifier and Type	Method and Description
void	DatasetRDFWriter.setCompoundReporter(CompoundURIReporter<net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> compoundReporter)

Constructor parameters in ambit2.rest.dataset with type arguments of type IStructureRecord

Constructor and Description
DatasetRDFWriter(CompoundURIReporter<net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> compoundReporter, PropertyURIReporter propertyReporter)
DatasetRDFWriter(CompoundURIReporter<net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> compoundReporter, PropertyURIReporter propertyReporter, net.idea.restnet.db.QueryURIReporter<IStructureRecord,net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> uriReporter)
DatasetRDFWriter(CompoundURIReporter<net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> compoundReporter, PropertyURIReporter propertyReporter, net.idea.restnet.db.QueryURIReporter<IStructureRecord,net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> uriReporter)
DatasetRDFWriter(CompoundURIReporter<net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> compoundReporter, PropertyURIReporter propertyReporter, net.idea.restnet.db.QueryURIReporter<IStructureRecord,net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> uriReporter)

Uses of IStructureRecord in ambit2.rest.model.builder

Methods in ambit2.rest.model.builder with parameters of type IStructureRecord

Modifier and Type	Method and Description
void	AbstractStructuresModelBuilder.transform(IStructureRecord[] records)
void	SMSDModelBuilder.transform(IStructureRecord[] records)

Uses of IStructureRecord in ambit2.rest.model.predictor

Classes in ambit2.rest.model.predictor with type parameters of type IStructureRecord

Modifier and Type	Class and Description
class	DescriptorPredictor<C extends net.idea.modbcum.p.AbstractDBProcessor<IStructureRecord,IStructureRecord>>
class	DescriptorPredictor<C extends net.idea.modbcum.p.AbstractDBProcessor<IStructureRecord,IStructureRecord>>

Fields in ambit2.rest.model.predictor declared as IStructureRecord

Modifier and Type	Field and Description
protected IStructureRecord	ModelPredictor.record

Methods in ambit2.rest.model.predictor that return IStructureRecord

Modifier and Type	Method and Description
IStructureRecord	ExternalModelPredictor.process(IStructureRecord target)
IStructureRecord	FingerprintsPredictor.process(IStructureRecord target)
IStructureRecord	ModelPredictor.process(NativeTypeItem target)

Methods in ambit2.rest.model.predictor with parameters of type IStructureRecord

Modifier and Type	Method and Description
void	AbstractStructureProcessor.assignResults(IStructureRecord record, Object value)
void	CoveragePredictor.assignResults(IStructureRecord record, Object value)
void	ExternalModelPredictor.assignResults(IStructureRecord record, Object value)
void	ModelPredictor.assignResults(IStructureRecord record, Object value)
protected void	NumericADPredictor.extractRecordID(IStructureRecord target, String url, IStructureRecord record)
protected void	ExpertModelpredictor.extractRecordID(IStructureRecord target, String url, IStructureRecord record)
protected void	ExternalModelPredictor.extractRecordID(IStructureRecord target, String url, IStructureRecord record)
protected void	ModelPredictor.extractRecordID(NativeTypeItem target, String url, IStructureRecord record)
protected Jama.Matrix	NumericADPredictor.getAsMatrix(IStructureRecord target)
String	NumericADPredictor.getCompoundURL(IStructureRecord target)
String	AbstractStructureProcessor.getCompoundURL(IStructureRecord target)
String	DescriptorPredictor.getCompoundURL(IStructureRecord target)
String	ExpertModelpredictor.getCompoundURL(IStructureRecord target)
String	ExternalModelPredictor.getCompoundURL(IStructureRecord target)
String	FingerprintsPredictor.getCompoundURL(IStructureRecord target)
Object	AbstractStructureProcessor.predict(IStructureRecord target)
Object	DescriptorPredictor.predict(IStructureRecord target)
Object	ExpertModelpredictor.predict(IStructureRecord target)
abstract OUTPUT	ExternalModel.predict(IStructureRecord record)
Object	ExternalModelPredictor.predict(IStructureRecord target)
Object	Structure2DProcessor.predict(IStructureRecord target)
Object	StructureProcessor.predict(IStructureRecord target)
protected double[][]	NumericADPredictor.predictionInstanceAsArray(IStructureRecord target)
IStructureRecord	ExternalModelPredictor.process(IStructureRecord target)
IStructureRecord	FingerprintsPredictor.process(IStructureRecord target)
protected Jama.Matrix	NumericADPredictor.transform(IStructureRecord target)
protected List<BitSet>	FingerprintsPredictor.transform(IStructureRecord target)

Uses of IStructureRecord in ambit2.rest.model.task

Methods in ambit2.rest.model.task that return types with arguments of type IStructureRecord

Modifier and Type	Method and Description
protected net.idea.modbcum.i.processors.ProcessorsChain<IStructureRecord,net.idea.modbcum.i.batch.IBatchStatistics,net.idea.modbcum.i.processors.IProcessor>	CallableModelPredictor.createProcessors()
protected net.idea.modbcum.i.processors.IProcessor<IStructureRecord,IStructureRecord>	CallableModelPredictor.getValuesReader()
protected net.idea.modbcum.i.processors.IProcessor<IStructureRecord,IStructureRecord>	CallableModelPredictor.getValuesReader()
protected net.idea.modbcum.i.processors.IProcessor<IStructureRecord,IStructureRecord>	CallableModelPredictor.getWriter()
protected net.idea.modbcum.i.processors.IProcessor<IStructureRecord,IStructureRecord>	CallableModelPredictor.getWriter()

Uses of IStructureRecord in ambit2.rest.rdf

Methods in ambit2.rest.rdf that return IStructureRecord

Modifier and Type	Method and Description
protected IStructureRecord	RDFStructuresIterator.createRecord()

Methods in ambit2.rest.rdf with parameters of type IStructureRecord

Modifier and Type	Method and Description
protected void	RDFStructuresIterator.parseFeatureValues(com.hp.hpl.jena.rdf.model.Resource dataEntry, IStructureRecord record)
boolean	RDFStructuresIterator.readStructure(com.hp.hpl.jena.rdf.model.RDFNode target, IStructureRecord record)
protected void	RDFStructuresIterator.setFeatureValue(IStructureRecord record, Property key, com.hp.hpl.jena.rdf.model.RDFNode value)

Uses of IStructureRecord in ambit2.rest.rdf.chembl

Fields in ambit2.rest.rdf.chembl declared as IStructureRecord

Modifier and Type	Field and Description
protected IStructureRecord	ChEMBLRawReader.record

Methods in ambit2.rest.rdf.chembl that return IStructureRecord

Modifier and Type	Method and Description
IStructureRecord	ChEMBLRawReader.nextRecord()
IStructureRecord	ChEMBLRawReader.processSolution(com.hp.hpl.jena.query.QuerySolution row)

Uses of IStructureRecord in ambit2.rest.rdf.sparql

Methods in ambit2.rest.rdf.sparql that return IStructureRecord

Modifier and Type	Method and Description
protected IStructureRecord	RDFCompoundIterator.newCompound(com.hp.hpl.jena.rdf.model.RDFNode node)

Methods in ambit2.rest.rdf.sparql with parameters of type IStructureRecord

Modifier and Type	Method and Description
protected void	RDFCompoundIterator.setCompoundIDS(IStructureRecord compound, int idchemical, int idstructure)
protected void	RDFCompoundIterator.setValue(IStructureRecord record, Property property, double value)
protected void	RDFCompoundIterator.setValue(IStructureRecord record, Property property, float value)
protected void	RDFCompoundIterator.setValue(IStructureRecord record, Property property, int value)
protected void	RDFCompoundIterator.setValue(IStructureRecord record, Property property, String value)

Uses of IStructureRecord in ambit2.rest.structure

Classes in ambit2.rest.structure with type parameters of type IStructureRecord

Modifier and Type	Class and Description
class	CompoundURIReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> MediaType.TEXT_URI_LIST
class	ConformerURIReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>> Generates conformer URI as /compound/{id}/conformer/{id}

Methods in ambit2.rest.structure that return types with arguments of type IStructureRecord

Modifier and Type	Method and Description
protected net.idea.modbcum.p.batch.AbstractBatchProcessor<net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,IStructureRecord>	CompoundURIReporter.createBatch(Q query)
protected net.idea.modbcum.p.batch.AbstractBatchProcessor<net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,IStructureRecord>	CompoundURIReporter.createBatch(Q query)

Methods in ambit2.rest.structure with parameters of type IStructureRecord

Modifier and Type	Method and Description
String	CompoundURIReporter.getURI(String ref, IStructureRecord item)
String	ConformerURIReporter.getURI(String ref, IStructureRecord item)

Uses of IStructureRecord in ambit2.rest.task.weka

Methods in ambit2.rest.task.weka with parameters of type IStructureRecord

Modifier and Type	Method and Description
void	FilteredWekaPredictor.assignResults(IStructureRecord record, Object value)
void	WekaPredictor.assignResults(IStructureRecord record, Object value)
void	FilteredWekaPredictor.assignTransformedInstance(IStructureRecord record, weka.core.Instance value, double confidence)
void	WekaPredictor.assignTransformedInstance(IStructureRecord record, weka.core.Instance value, double confidence)

Uses of IStructureRecord in ambit2.sln.io

Methods in ambit2.sln.io that return IStructureRecord

Modifier and Type	Method and Description
IStructureRecord	SLN2Substance.slnContainerToStructureRecord(SLNContainer slnContainer)

Methods in ambit2.sln.io with parameters of type IStructureRecord

Modifier and Type	Method and Description
SLNContainer	SLN2Substance.structureRecordToSLNContainer(IStructureRecord structure)

Uses of IStructureRecord in ambit2.ui.table

Fields in ambit2.ui.table with type parameters of type IStructureRecord

Modifier and Type	Field and Description
protected List<IStructureRecord>	StructureRecordsTableModel.records

Methods in ambit2.ui.table that return types with arguments of type IStructureRecord

Modifier and Type	Method and Description
List<IStructureRecord>	StructureRecordsTableModel.getRecords()

Method parameters in ambit2.ui.table with type arguments of type IStructureRecord

Modifier and Type	Method and Description
void	StructureRecordsTableModel.setRecords(List<IStructureRecord> records)

Uses of IStructureRecord in ambit2.vega

Methods in ambit2.vega with parameters of type IStructureRecord

Modifier and Type	Method and Description
org.openscience.cdk.interfaces.IAtomContainer	ExternalModelVega.predict(IStructureRecord record)