Uses of Class org.bridgedb.DataSource (BridgeDb 3.0.18 API)

Packages that use DataSource
Package	Description
org.bridgedb	BridgeDb is a java library intended for dealing with identifiers for biological entities such as genes, proteins, metabolites.
org.bridgedb.file	Driver and helper classes for using simple files as an identifier mapping service.
org.bridgedb.impl

Uses of DataSource in org.bridgedb

Methods in org.bridgedb that return DataSource
Modifier and Type	Method	Description
`DataSource`	DataSource.Builder.`asDataSource()`
`static DataSource`	DataSource.`getByAlias(String alias)`
`static DataSource`	DataSource.`getByCompactIdentifierPrefix(String prefix)`
`static DataSource`	DataSource.`getByIdentiferOrgBase(String base)`	Since version 2.0 this method will return null if no DataSource is known
`static DataSource`	DataSource.`getByMiriamBase(String base)`	Since version 2.0 this method will return null if no DataSource is known
`DataSource`	Xref.`getDataSource()`
`static DataSource`	DataSource.`getExistingByBioregistryPrefix(String prefix)`
`static DataSource`	DataSource.`getExistingByFullName(String fullName)`	returns pre-existing DataSource object
`static DataSource`	DataSource.`getExistingBySystemCode(String systemCode)`
`DataSource`	DataSource.`isDeprecatedBy()`	Returns the DataSource that should be used instead if this DataSource is deprecated.

Methods in org.bridgedb that return types with arguments of type DataSource
Modifier and Type	Method	Description
`static Set<DataSource>`	DataSourcePatterns.`getDataSourceMatches(String id)`	Look for all DataSource patterns that match a given input.
`static Set<DataSource>`	DataSource.`getDataSources()`	get all registered datasoures as a set.
`static Set<DataSource>`	DataSource.`getFilteredSet(Boolean primary, Boolean metabolite, Object o)`	returns a filtered subset of available datasources.
`static Map<DataSource,Pattern>`	DataSourcePatterns.`getPatterns()`
`Set<DataSource>`	AbstractIDMapperCapabilities.`getSupportedSrcDataSources()`
`Set<DataSource>`	IDMapperCapabilities.`getSupportedSrcDataSources()`
`Set<DataSource>`	AbstractIDMapperCapabilities.`getSupportedTgtDataSources()`
`Set<DataSource>`	IDMapperCapabilities.`getSupportedTgtDataSources()`

Methods in org.bridgedb with parameters of type DataSource
Modifier and Type	Method	Description
`DataSource.Builder`	DataSource.Builder.`deprecatedBy(DataSource sourceToUseInstead)`	Sets the DataSource which should be used instead of this deprecated one.
`Set<String>`	IDMapperStack.`getAttributesForAllMappings(Xref ref, String attrname, DataSource... dataSources)`
`Map<String,Set<String>>`	IDMapperStack.`getAttributesForAllMappings(Xref ref, DataSource... dataSources)`
`Iterable<Xref>`	XrefIterator.`getIterator(DataSource ds)`	Create an iterator that iterates over all Xrefs of a certain DataSource defined by this IDMapper.
`boolean`	AbstractIDMapperCapabilities.`isMappingSupported(DataSource src, DataSource tgt)`
`boolean`	IDMapperCapabilities.`isMappingSupported(DataSource src, DataSource tgt)`
`Set<Xref>`	AbstractIDMapper.`mapID(Xref srcRef, DataSource... tgtDataSources)`	Default implementation of mapID.
`Map<Xref,Set<Xref>>`	IDMapper.`mapID(Collection<Xref> srcXrefs, DataSource... tgtDataSources)`	Get all cross-references for a set of entities, restricting the result to contain only references from the given set of data sources.
`Set<Xref>`	IDMapper.`mapID(Xref ref, DataSource... tgtDataSources)`	Get all cross-references for the given entity, restricting the result to contain only references from the given set of data sources.
`Map<Xref,Set<Xref>>`	IDMapperStack.`mapID(Collection<Xref> srcXrefs, DataSource... tgtDataSources)`	Get all cross-references for a set of entities, restricting the result to contain only references from the given set of data sources.
`Set<Xref>`	IDMapperStack.`mapID(Xref ref, DataSource... resultDs)`	Get all cross-references for the given entity, restricting the result to contain only references from the given set of data sources.
`static void`	DataSourcePatterns.`registerPattern(DataSource key, Pattern value)`	Register a regex Pattern for recognizing a DataSource.

Constructors in org.bridgedb with parameters of type DataSource
Constructor	Description
`Xref(String id, DataSource ds)`
`Xref(String id, DataSource ds, boolean isPrimary)`

Constructor parameters in org.bridgedb with type arguments of type DataSource
Constructor	Description
`AbstractIDMapperCapabilities(Set<DataSource> supportedDataSources, boolean freeSearchSupported, Map<String,String> props)`

Uses of DataSource in org.bridgedb.file

Methods in org.bridgedb.file that return types with arguments of type DataSource
Modifier and Type	Method	Description
`Set<DataSource>`	IDMappingReader.`getDataSources()`	Get `DataSource`s from the file.
`Set<DataSource>`	IDMappingReaderFromDelimitedReader.`getDataSources()`	Get `DataSource`s from the file.

Methods in org.bridgedb.file with parameters of type DataSource
Modifier and Type	Method	Description
`Map<Xref,Set<Xref>>`	IDMapperFile.`mapID(Collection<Xref> srcXrefs, DataSource... tgtDataSources)`	Get all cross-references for a set of entities, restricting the result to contain only references from the given set of data sources.
`Set<Xref>`	IDMapperFile.`mapID(Xref srcXref, DataSource... tgtDataSources)`	Get all cross-references for the given entity, restricting the result to contain only references from the given set of data sources.

Method parameters in org.bridgedb.file with type arguments of type DataSource
Modifier and Type	Method	Description
`void`	IDMappingReaderFromDelimitedReader.`setDataSources(List<DataSource> dataSources)`	Set `DataSource`s.

Uses of DataSource in org.bridgedb.impl

Methods in org.bridgedb.impl that return types with arguments of type DataSource
Modifier and Type	Method	Description
`static Map<DataSource,Set<Xref>>`	InternalUtils.`groupByDataSource(Collection<Xref> srcXrefs)`	Split a heterogeneous `Xref` set into multiple homogeneous Xref sets.

Methods in org.bridgedb.impl with parameters of type DataSource
Modifier and Type	Method	Description
`boolean`	TransitiveGraph.`isTransitiveMappingSupported(DataSource src, DataSource tgt)`
`static Map<Xref,Set<Xref>>`	InternalUtils.`mapMultiFromSingle(IDMapper mapper, Collection<Xref> srcXrefs, DataSource... tgt)`	call the "single" mapID (Xref, ...) multiple times to perform mapping of a Set.
`static Set<Xref>`	InternalUtils.`mapSingleFromMulti(IDMapper mapper, Xref src, DataSource... tgt)`	call the "multi" mapID (Set, ...) using a Set with one item to perform mapping of a single ID.

Method parameters in org.bridgedb.impl with type arguments of type DataSource
Modifier and Type	Method	Description
`Set<Xref>`	TransitiveGraph.`mapIDtransitiveTargetted(Xref ref, Set<DataSource> dsFilter)`
`void`	TransitiveGraph.`printMap(Map<DataSource,Set<org.bridgedb.impl.TransitiveGraph.Path>> map)`	This is for testing.