Uses of Class
org.bridgedb.Xref

Packages that use Xref

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 Xref in org.bridgedb

Methods in org.bridgedb that return Xref

Modifier and Type	Method and Description
static Xref	Xref.fromCompactIdentifier(String compact) This method will convert a compact identifier to an Xref
static Xref	Xref.fromMiriamUrn(String urn) This method will convert a known Miriam Urn to an Xref
Xref	DataSource.getExample()

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

Modifier and Type	Method and Description
Map<Xref,String>	IDMapperStack.freeAttributeSearch(String query, String attrType, int limit) free text search for matching attributes.
Map<Xref,String>	AttributeMapper.freeAttributeSearch(String query, String attrType, int limit) free text search for matching attributes.
Map<Xref,Set<String>>	IDMapperStack.freeAttributeSearchEx(String query, String attrType, int limit)
Map<Xref,Set<String>>	AttributeMapper.freeAttributeSearchEx(String query, String attrType, int limit) Improved version of free text search for matching attributes.
Set<Xref>	IDMapperStack.freeSearch(String text, int limit) free text search for matching symbols or identifiers.
Set<Xref>	IDMapper.freeSearch(String text, int limit) free text search for matching symbols or identifiers.
Iterable<Xref>	XrefIterator.getIterator() Create an iterator that iterates over all Xrefs defined by this IDMapper.
Iterable<Xref>	XrefIterator.getIterator(DataSource ds) Create an iterator that iterates over all Xrefs of a certain DataSource defined by this IDMapper.
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>>	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.
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.

Methods in org.bridgedb with parameters of type Xref

Modifier and Type	Method and Description
int	Xref.compareTo(Xref idc) Compares two Xrefs, asciibetically using string representation.
Map<String,Set<String>>	IDMapperStack.getAttributes(Xref ref) Get all attributes for an entity.
Map<String,Set<String>>	AttributeMapper.getAttributes(Xref ref) Get all attributes for an entity.
Set<String>	IDMapperStack.getAttributes(Xref ref, String attrname) Get attributes for an entity, such as gene Symbol.
Set<String>	AttributeMapper.getAttributes(Xref ref, String attrType) Get attributes for an entity, such as gene Symbol.
Map<String,Set<String>>	IDMapperStack.getAttributesForAllMappings(Xref ref, DataSource... dataSources)
Set<String>	IDMapperStack.getAttributesForAllMappings(Xref ref, String attrname, DataSource... dataSources)
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.
boolean	IDMapperStack.xrefExists(Xref xref) Check whether an Xref is known by the given mapping source.
boolean	IDMapper.xrefExists(Xref xref) Check whether an Xref is known by the given mapping source.

Method parameters in org.bridgedb with type arguments of type Xref

Modifier and Type	Method and Description
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.

Uses of Xref in org.bridgedb.file

Methods in org.bridgedb.file that return types with arguments of type Xref

Modifier and Type	Method and Description
Set<Xref>	IDMapperText.freeSearch(String text, int limit) Free search is not supported for delimiter-text file.
Map<Xref,Set<Xref>>	IDMappingReader.getIDMappings() Get Xrefs from the file.
Map<Xref,Set<Xref>>	IDMappingReader.getIDMappings() Get Xrefs from the file.
Map<Xref,Set<Xref>>	IDMappingReaderFromDelimitedReader.getIDMappings() Get Xrefs from the file.
Map<Xref,Set<Xref>>	IDMappingReaderFromDelimitedReader.getIDMappings() Get Xrefs from the file.
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.
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.

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

Modifier and Type	Method and Description
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.
boolean	IDMapperFile.xrefExists(Xref xref) Check whether an Xref is known by the given mapping source.

Method parameters in org.bridgedb.file with type arguments of type Xref

Modifier and Type	Method and Description
protected void	IDMappingReaderFromDelimitedReader.addIDMapping(Set<Xref> xrefs) Add matched references.
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.

Uses of Xref in org.bridgedb.impl

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

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.
Set<Xref>	TransitiveGraph.mapIDtransitiveTargetted(Xref ref, Set<DataSource> dsFilter)
Set<Xref>	TransitiveGraph.mapIDtransitiveUntargetted(Xref ref)
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 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.

Methods in org.bridgedb.impl with parameters of type Xref

Modifier and Type	Method and Description
Set<Xref>	TransitiveGraph.mapIDtransitiveTargetted(Xref ref, Set<DataSource> dsFilter)
Set<Xref>	TransitiveGraph.mapIDtransitiveUntargetted(Xref ref)
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 Xref

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.
static String	InternalUtils.joinIds(Collection<Xref> refs, String sep) Join the ID part of a collection of Xrefs with a custom separator.
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.