Uses of Class
org.bridgedb.DataSource

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 and Description
DataSource	DataSource.Builder.asDataSource()
static DataSource	DataSource.getByAlias(String alias)
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.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 and 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 and Description
DataSource.Builder	DataSource.Builder.deprecatedBy(DataSource sourceToUseInstead) Sets the DataSource which should be used instead of this deprecated one.
Map<String,Set<String>>	IDMapperStack.getAttributesForAllMappings(Xref ref, DataSource... dataSources)
Set<String>	IDMapperStack.getAttributesForAllMappings(Xref ref, String attrname, 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)
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.
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>	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.
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.
Set<Xref>	AbstractIDMapper.mapID(Xref srcRef, DataSource... tgtDataSources) Default implementation of mapID.
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 and 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 and 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 and Description
Set<DataSource>	IDMappingReader.getDataSources() Get DataSources from the file.
Set<DataSource>	IDMappingReaderFromDelimitedReader.getDataSources() Get DataSources from the file.

Methods in org.bridgedb.file with parameters of type DataSource

Modifier and Type	Method and 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 and Description
void	IDMappingReaderFromDelimitedReader.setDataSources(List<DataSource> dataSources) Set DataSources.

Uses of DataSource in org.bridgedb.impl

Methods in org.bridgedb.impl that return types with arguments of type DataSource

Modifier and Type	Method and 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 and 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 and 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.