Index (BridgeDb 3.0.17 API)

A B C D E F G H I J M N O P R S T U X
All Classes All Packages

A

AbstractIDMapper - Class in org.bridgedb: Contains default implementation of some IDMapper methods.
AbstractIDMapper() - Constructor for class org.bridgedb.AbstractIDMapper
AbstractIDMapperCapabilities - Class in org.bridgedb: Simple implementation of IDMapperCapabilities, which assumes that the supported datasources are the same for target and source, and that the supported data sources and properties are static and known at creation time.
AbstractIDMapperCapabilities(Set<DataSource>, boolean, Map<String, String>) - Constructor for class org.bridgedb.AbstractIDMapperCapabilities
add(String, String, String) - Method in class buildsystem.Measure
addIDMapper(String) - Method in class org.bridgedb.IDMapperStack: Create a fresh IDMapper from a connectionString and add it to the stack.
addIDMapper(IDMapper) - Method in class org.bridgedb.IDMapperStack: Add an existing IDMapper to the stack.
addIDMapping(Set<Xref>) - Method in class org.bridgedb.file.IDMappingReaderFromDelimitedReader: Add matched references.
alternative(String) - Method in class org.bridgedb.DataSource.Builder: Allow the setting but not changing of an alternative name
asDataSource() - Method in class org.bridgedb.DataSource.Builder
AttributeMapper - Interface in org.bridgedb: AttributeMapper knows about attributes for Xrefs.

B

bioregistryPrefix(String) - Method in class org.bridgedb.DataSource.Builder
BioregistryResolver - Class in org.bridgedb.resolvers
BridgeDb - Class in org.bridgedb: Central access point for connecting to IDMappers.
buildsystem - package buildsystem

C

cap - Variable in class org.bridgedb.file.IDMapperFile
categories(String) - Method in class org.bridgedb.DataSource.Builder
categories(String[]) - Method in class org.bridgedb.DataSource.Builder
close() - Method in class org.bridgedb.file.IDMapperFile: dispose any resources (such as open database connections) associated with this IDMapper.
close() - Method in interface org.bridgedb.IDMapper: dispose any resources (such as open database connections) associated with this IDMapper.
close() - Method in class org.bridgedb.IDMapperStack: closes all child databases.
compactIdentifierPrefix(String) - Method in class org.bridgedb.DataSource.Builder
compareTo(Xref) - Method in class org.bridgedb.Xref: Compares two Xrefs, asciibetically using string representation.
connect(String) - Static method in class org.bridgedb.BridgeDb: Finds the correct implementation of the IDMapper interface and instantiates it.
connect(String) - Method in interface org.bridgedb.Driver: Never call this method directly, use BridgeDb.connect(java.lang.String) instead.

D

DataSource - Class in org.bridgedb: Contains information about a certain DataSource.
DataSource.Builder - Class in org.bridgedb: Uses builder pattern to set optional attributes for a DataSource.
DataSourcePatterns - Class in org.bridgedb: Contains regular expression patterns for identifiers Can be used to guess the BioDataSource of an identifier of unknown origin.
deprecated(boolean) - Method in class org.bridgedb.DataSource.Builder
deprecatedBy(DataSource) - Method in class org.bridgedb.DataSource.Builder: Sets the DataSource which should be used instead of this deprecated one.
description(String) - Method in class org.bridgedb.DataSource.Builder: Allow the setting but not changing of a description
Driver - Interface in org.bridgedb: A Driver knows how to create an IDMapper instance.
dsValid - Variable in class org.bridgedb.file.IDMappingReaderFromDelimitedReader

E

equals(Object) - Method in class org.bridgedb.Xref

F

freeAttributeSearch(String, String, int) - Method in interface org.bridgedb.AttributeMapper: free text search for matching attributes.
freeAttributeSearch(String, String, int) - Method in class org.bridgedb.IDMapperStack: free text search for matching attributes.
freeAttributeSearchEx(String, String, int) - Method in interface org.bridgedb.AttributeMapper: Improved version of free text search for matching attributes.
freeAttributeSearchEx(String, String, int) - Method in class org.bridgedb.IDMapperStack
freeSearch(String, int) - Method in class org.bridgedb.file.IDMapperText: Free search is not supported for delimiter-text file.
freeSearch(String, int) - Method in interface org.bridgedb.IDMapper: free text search for matching symbols or identifiers.
freeSearch(String, int) - Method in class org.bridgedb.IDMapperStack: free text search for matching symbols or identifiers.
fromBioregistryIdentifier(String) - Static method in class org.bridgedb.Xref: This method will convert a Bioregistry.io identifier to an Xref.
fromCompactIdentifier(String) - Static method in class org.bridgedb.Xref: This method will convert a compact identifier to an Xref.
fromMiriamUrn(String) - Static method in class org.bridgedb.Xref: This method will convert a known Miriam Urn to an Xref
fullNameExists(String) - Static method in class org.bridgedb.DataSource: Check if a DataSoucre with this sfullName has been registered

G

getAlternative() - Method in class org.bridgedb.DataSource: Retrieves any saved alternative name.
getAttributes(Xref) - Method in interface org.bridgedb.AttributeMapper: Get all attributes for an entity.
getAttributes(Xref) - Method in class org.bridgedb.IDMapperStack: Get all attributes for an entity.
getAttributes(Xref, String) - Method in interface org.bridgedb.AttributeMapper: Get attributes for an entity, such as gene Symbol.
getAttributes(Xref, String) - Method in class org.bridgedb.IDMapperStack: Get attributes for an entity, such as gene Symbol.
getAttributeSet() - Method in interface org.bridgedb.AttributeMapper: Set of attributes provided by this AttributeMapper.
getAttributeSet() - Method in class org.bridgedb.IDMapperStack: Set of attributes provided by this AttributeMapper.
getAttributesForAllMappings(Xref, String, DataSource...) - Method in class org.bridgedb.IDMapperStack
getAttributesForAllMappings(Xref, DataSource...) - Method in class org.bridgedb.IDMapperStack
getBioregistryIdentifier() - Method in class org.bridgedb.Xref: Uses DataSource.getCompactidentifier() to create a compact identifier, such as uniprot:P12345.
getBioregistryIdentifier(String) - Method in class org.bridgedb.DataSource: Creates a Bioregistry.io compact identifier.
getBioregistryPrefix() - Method in class org.bridgedb.DataSource
getByAlias(String) - Static method in class org.bridgedb.DataSource
getByCompactIdentifierPrefix(String) - Static method in class org.bridgedb.DataSource
getByIdentiferOrgBase(String) - Static method in class org.bridgedb.DataSource: Since version 2.0 this method will return null if no DataSource is known
getByMiriamBase(String) - Static method in class org.bridgedb.DataSource: Since version 2.0 this method will return null if no DataSource is known
getCapabilities() - Method in class org.bridgedb.file.IDMapperFile
getCapabilities() - Method in interface org.bridgedb.IDMapper
getCapabilities() - Method in class org.bridgedb.IDMapperStack
getCategories() - Method in class org.bridgedb.DataSource
getCompactidentifier() - Method in class org.bridgedb.Xref: Uses DataSource.getCompactidentifier() to create a compact identifier, such as uniprot:P12345.
getCompactIdentifier(String) - Method in class org.bridgedb.DataSource: Creates a compact identifier.
getCompactIdentifierPrefix() - Method in class org.bridgedb.DataSource: Returns the compact identifier prefix (previously known as MIRIAM base.
getDataSource() - Method in class org.bridgedb.Xref
getDataSourceDelimiters() - Method in class org.bridgedb.file.IDMapperText
getDataSourceMatches(String) - Static method in class org.bridgedb.DataSourcePatterns: Look for all DataSource patterns that match a given input.
getDataSources() - Static method in class org.bridgedb.DataSource: get all registered datasoures as a set.
getDataSources() - Method in interface org.bridgedb.file.IDMappingReader: Get DataSources from the file.
getDataSources() - Method in class org.bridgedb.file.IDMappingReaderFromDelimitedReader: Get DataSources from the file.
getDescription() - Method in class org.bridgedb.DataSource: Retrieves any saved description.
getExample() - Method in class org.bridgedb.DataSource
getExistingByBioregistryPrefix(String) - Static method in class org.bridgedb.DataSource
getExistingByFullName(String) - Static method in class org.bridgedb.DataSource: returns pre-existing DataSource object
getExistingBySystemCode(String) - Static method in class org.bridgedb.DataSource
getFilteredSet(Boolean, Boolean, Object) - Static method in class org.bridgedb.DataSource: returns a filtered subset of available datasources.
getFullName() - Method in class org.bridgedb.DataSource: returns full name of DataSource e.g.
getFullNames() - Static method in class org.bridgedb.DataSource: Get a list of all non-null full names.
getId() - Method in class org.bridgedb.Xref
getIDDelimiters() - Method in class org.bridgedb.file.IDMapperText
getIdentifiersOrgUri(String) - Method in class org.bridgedb.DataSource
getIDMapperAt(int) - Method in class org.bridgedb.IDMapperStack
getIDMappingReader() - Method in class org.bridgedb.file.IDMapperFile
getIDMappings() - Method in interface org.bridgedb.file.IDMappingReader: Get Xrefs from the file.
getIDMappings() - Method in class org.bridgedb.file.IDMappingReaderFromDelimitedReader: Get Xrefs from the file.
getInputStream(String) - Static method in class org.bridgedb.impl.InternalUtils
getInputStream(URL) - Static method in class org.bridgedb.impl.InternalUtils: Start downloading a file from the web and open an InputStream to it.
getInstance() - Static method in class org.bridgedb.resolvers.BioregistryResolver
getInstance() - Static method in class org.bridgedb.resolvers.IdentifiersDotOrgResolver
getInstance() - Static method in class org.bridgedb.resolvers.Names2ThingsResolver
getIterator() - Method in interface org.bridgedb.XrefIterator: Create an iterator that iterates over all Xrefs defined by this IDMapper.
getIterator(DataSource) - Method in interface org.bridgedb.XrefIterator: Create an iterator that iterates over all Xrefs of a certain DataSource defined by this IDMapper.
getKeys() - Method in class org.bridgedb.AbstractIDMapperCapabilities
getKeys() - Method in interface org.bridgedb.IDMapperCapabilities
getKnownUrl() - Method in class org.bridgedb.Xref: Uses DataSource.getKnownUrl to create a valid URL for an online webpage describing this entity.
getKnownUrl(String) - Method in class org.bridgedb.DataSource: Turn id into url pointing to info page on the web, e.g.
getMainUrl() - Method in class org.bridgedb.DataSource: Return the main Url for this datasource, that can be used to refer to the datasource in general.
getMappers() - Method in class org.bridgedb.IDMapperStack: get all mappers
getMiriamURN() - Method in class org.bridgedb.Xref: Uses DataSource.getMiriamURN() to create a global identifier, such as urn:miriam:uniprot:P12345.
getMiriamURN(String) - Method in class org.bridgedb.DataSource: Creates a global identifier.
getOrganism() - Method in class org.bridgedb.DataSource
getPatterns() - Static method in class org.bridgedb.DataSourcePatterns
getProperty(String) - Method in class org.bridgedb.AbstractIDMapperCapabilities: Return a value for a property, or null if this property is not defined.
getProperty(String) - Method in interface org.bridgedb.IDMapperCapabilities: Return a value for a property, or null if this property is not defined.
getSize() - Method in class org.bridgedb.IDMapperStack
getSupportedSrcDataSources() - Method in class org.bridgedb.AbstractIDMapperCapabilities
getSupportedSrcDataSources() - Method in interface org.bridgedb.IDMapperCapabilities
getSupportedTgtDataSources() - Method in class org.bridgedb.AbstractIDMapperCapabilities
getSupportedTgtDataSources() - Method in interface org.bridgedb.IDMapperCapabilities
getSystemCode() - Method in class org.bridgedb.DataSource: returns GenMAPP SystemCode, e.g.
getTransitive() - Method in class org.bridgedb.IDMapperStack
getTransitivity() - Method in class org.bridgedb.file.IDMapperText: Get transitivity support.
getTransitivity() - Method in class org.bridgedb.file.IDMappingReaderFromDelimitedReader: Get transitivity support.
getType() - Method in class org.bridgedb.DataSource
getURL() - Method in class org.bridgedb.file.IDMapperText: Get URL of the file.
getURL(Xref) - Method in class org.bridgedb.resolvers.BioregistryResolver
getURL(Xref) - Method in class org.bridgedb.resolvers.IdentifiersDotOrgResolver
getURL(Xref) - Method in interface org.bridgedb.resolvers.IResolver: Returns a URL to resolve the identifier for this service.
getURL(Xref) - Method in class org.bridgedb.resolvers.Names2ThingsResolver
groupByDataSource(Collection<Xref>) - Static method in class org.bridgedb.impl.InternalUtils: Split a heterogeneous Xref set into multiple homogeneous Xref sets.

H

hashCode() - Method in class org.bridgedb.Xref: hashCode calculated from id and datasource combined.

I

IdentifiersDotOrgResolver - Class in org.bridgedb.resolvers
identifiersOrgBase(String) - Method in class org.bridgedb.DataSource.Builder: Note: Since version 2 The base must start with urn:miriam:.
idExample(String) - Method in class org.bridgedb.DataSource.Builder: Note: Unlike most builder methods this one does allow the idExample to be change even if already set.
IDMapper - Interface in org.bridgedb: Base interface for all id mapping methods.
IDMapperCapabilities - Interface in org.bridgedb: Describes capabilities of an IDMapper.
IDMapperException - Exception in org.bridgedb: for all exceptions thrown by IDMapper interface.
IDMapperException() - Constructor for exception org.bridgedb.IDMapperException: See Exception ().
IDMapperException(String) - Constructor for exception org.bridgedb.IDMapperException: See Exception (String).
IDMapperException(String, Throwable) - Constructor for exception org.bridgedb.IDMapperException: See Exception(String, Throwable).
IDMapperException(Throwable) - Constructor for exception org.bridgedb.IDMapperException: See Exception(Throwable).
IDMapperFile - Class in org.bridgedb.file: Interface for ID mapping from files.
IDMapperFile(IDMappingReader) - Constructor for class org.bridgedb.file.IDMapperFile: Constructor from a IDMappingReader.
IDMapperFile(IDMappingReader, boolean) - Constructor for class org.bridgedb.file.IDMapperFile: Constructor from a IDMappingReader and user-defined free search capacity.
IDMapperStack - Class in org.bridgedb: combines multiple IDMapper's in a stack.
IDMapperStack() - Constructor for class org.bridgedb.IDMapperStack
IDMapperText - Class in org.bridgedb.file: Class for mapping ID from delimited text file.
IDMapperText(URL) - Constructor for class org.bridgedb.file.IDMapperText: Constructor from the URL of a tab-delimited text file.
IDMapperText(URL, char[]) - Constructor for class org.bridgedb.file.IDMapperText: Transitivity is unsupported.
IDMapperText(URL, char[], char[]) - Constructor for class org.bridgedb.file.IDMapperText: Transitivity is unsupported.
IDMapperText(URL, char[], char[], boolean) - Constructor for class org.bridgedb.file.IDMapperText: Constructor from the URL of a tab-delimited text file, delimiters to separate between different data sources and IDs and transitivity support.
IDMapperWebservice - Class in org.bridgedb.webservice
IDMapperWebservice() - Constructor for class org.bridgedb.webservice.IDMapperWebservice
IDMappingReader - Interface in org.bridgedb.file: Interface for reading ID mapping data.
IDMappingReaderFromDelimitedReader - Class in org.bridgedb.file: Class for reading ID mapping data from delimited reader.
IDMappingReaderFromDelimitedReader(Reader, String, String, boolean) - Constructor for class org.bridgedb.file.IDMappingReaderFromDelimitedReader
IDMappingReaderFromText - Class in org.bridgedb.file: Class for reading ID mapping data from delimited text file.
IDMappingReaderFromText(URL, char[]) - Constructor for class org.bridgedb.file.IDMappingReaderFromText: Transitivity is unsupported.
IDMappingReaderFromText(URL, char[], char[]) - Constructor for class org.bridgedb.file.IDMappingReaderFromText: Transitivity is unsupported.
IDMappingReaderFromText(URL, char[], char[], boolean) - Constructor for class org.bridgedb.file.IDMappingReaderFromText: Constructor from the URL of a tab-delimited text file, delimiters to separate between different data sources and IDs and transitivity support.
IDMappingReaderFromText(URL, String) - Constructor for class org.bridgedb.file.IDMappingReaderFromText: Transitivity is unsupported.
IDMappingReaderFromText(URL, String, String) - Constructor for class org.bridgedb.file.IDMappingReaderFromText: Transitivity is unsupported.
IDMappingReaderFromText(URL, String, String, boolean) - Constructor for class org.bridgedb.file.IDMappingReaderFromText
idMappingValid - Variable in class org.bridgedb.file.IDMappingReaderFromDelimitedReader
InternalUtils - Class in org.bridgedb.impl: To prevent duplication and redundancy, functions that are common to multiple IDMapper implementations can be placed here.
IResolver - Interface in org.bridgedb.resolvers: Interface for compact identifier resolvers.
isConnected() - Method in class org.bridgedb.file.IDMapperFile: Use this method to check if the IDMapper is still valid.
isConnected() - Method in interface org.bridgedb.IDMapper: Use this method to check if the IDMapper is still valid.
isConnected() - Method in class org.bridgedb.IDMapperStack
isDeprecated() - Method in class org.bridgedb.DataSource: A DataSource is deprecated if it is replaced by another data source which should be used instead.
isDeprecatedBy() - Method in class org.bridgedb.DataSource: Returns the DataSource that should be used instead if this DataSource is deprecated.
isFreeAttributeSearchSupported() - Method in interface org.bridgedb.AttributeMapper
isFreeAttributeSearchSupported() - Method in class org.bridgedb.IDMapperStack
isFreeSearchSupported() - Method in class org.bridgedb.AbstractIDMapperCapabilities
isFreeSearchSupported() - Method in interface org.bridgedb.IDMapperCapabilities
isMappingSupported(DataSource, DataSource) - Method in class org.bridgedb.AbstractIDMapperCapabilities
isMappingSupported(DataSource, DataSource) - Method in interface org.bridgedb.IDMapperCapabilities
isMetabolite() - Method in class org.bridgedb.DataSource
isPrimary() - Method in class org.bridgedb.DataSource
isPrimary() - Method in class org.bridgedb.Xref
isTransitiveMappingSupported(DataSource, DataSource) - Method in class org.bridgedb.impl.TransitiveGraph

J

joinIds(Collection<Xref>, String) - Static method in class org.bridgedb.impl.InternalUtils: Join the ID part of a collection of Xrefs with a custom separator.

M

mainUrl(String) - Method in class org.bridgedb.DataSource.Builder: Note: Since version 2 this method no longer allows changing a mainUrl once set.
mapID(Collection<Xref>, DataSource...) - Method in class org.bridgedb.file.IDMapperFile: Get all cross-references for a set of entities, restricting the result to contain only references from the given set of data sources.
mapID(Collection<Xref>, DataSource...) - Method in interface org.bridgedb.IDMapper: Get all cross-references for a set of entities, restricting the result to contain only references from the given set of data sources.
mapID(Collection<Xref>, DataSource...) - Method in class org.bridgedb.IDMapperStack: Get all cross-references for a set of entities, restricting the result to contain only references from the given set of data sources.
mapID(Xref, DataSource...) - Method in class org.bridgedb.AbstractIDMapper: Default implementation of mapID.
mapID(Xref, DataSource...) - Method in class org.bridgedb.file.IDMapperFile: Get all cross-references for the given entity, restricting the result to contain only references from the given set of data sources.
mapID(Xref, DataSource...) - Method in interface org.bridgedb.IDMapper: Get all cross-references for the given entity, restricting the result to contain only references from the given set of data sources.
mapID(Xref, DataSource...) - Method in class org.bridgedb.IDMapperStack: Get all cross-references for the given entity, restricting the result to contain only references from the given set of data sources.
mapIDtransitiveTargetted(Xref, Set<DataSource>) - Method in class org.bridgedb.impl.TransitiveGraph
mapIDtransitiveUntargetted(Xref) - Method in class org.bridgedb.impl.TransitiveGraph
mapMultiFromSingle(IDMapper, Collection<Xref>, DataSource...) - Static method in class org.bridgedb.impl.InternalUtils: call the "single" mapID (Xref, ...) multiple times to perform mapping of a Set.
mapSingleFromMulti(IDMapper, Xref, DataSource...) - Static method in class org.bridgedb.impl.InternalUtils: call the "multi" mapID (Set, ...) using a Set with one item to perform mapping of a single ID.
MATCH_ID - Static variable in interface org.bridgedb.AttributeMapper: use this magic constant as the attrType parameter to also search for identifiers.
Measure - Class in buildsystem
Measure(String) - Constructor for class buildsystem.Measure
miriamBase(String) - Method in class org.bridgedb.DataSource.Builder
mock(String, String) - Static method in class org.bridgedb.DataSource: Create a new DataSource with (optional) detailed information with registration.
multiMapAdd(Map<T, List<U>>, T, U) - Static method in class org.bridgedb.impl.InternalUtils: Generic method for multimaps, a map that can contain multiple values per key.
multiMapPut(Map<T, Set<U>>, T, U) - Static method in class org.bridgedb.impl.InternalUtils: Generic method for multimaps, a map that can contain multiple values per key.
multiMapPutAll(Map<T, Set<U>>, T, Collection<U>) - Static method in class org.bridgedb.impl.InternalUtils: Generic method for multimaps, a map that can contain multiple values per key.

N

Names2ThingsResolver - Class in org.bridgedb.resolvers

O

org.bridgedb - package org.bridgedb: BridgeDb is a java library intended for dealing with identifiers for biological entities such as genes, proteins, metabolites.
org.bridgedb.file - package org.bridgedb.file: Driver and helper classes for using simple files as an identifier mapping service.
org.bridgedb.impl - package org.bridgedb.impl
org.bridgedb.resolvers - package org.bridgedb.resolvers
org.bridgedb.webservice - package org.bridgedb.webservice
organism(Object) - Method in class org.bridgedb.DataSource.Builder: Since version 2 This method no longer allows you to change the Organism of a DataSource once set.

P

parseLocation(String, String...) - Static method in class org.bridgedb.impl.InternalUtils: parse configuration params of the connection string.
primary(boolean) - Method in class org.bridgedb.DataSource.Builder: Note: Unlike most builder methods this one does allow the idPrimary to be change even if already set.
printMap(Map<DataSource, Set<TransitiveGraph.Path>>) - Method in class org.bridgedb.impl.TransitiveGraph: This is for testing.

R

readData(Reader) - Method in class org.bridgedb.file.IDMappingReaderFromDelimitedReader: Read data.
readDataSources() - Method in class org.bridgedb.file.IDMappingReaderFromDelimitedReader: Read DataSources from the reader.
reader - Variable in class org.bridgedb.file.IDMapperFile
readIDMappings() - Method in class org.bridgedb.file.IDMappingReaderFromDelimitedReader: Read ID mappings from the reader.
readXmlConfig(InputSource) - Static method in class org.bridgedb.impl.InternalUtils: read a configuration file in the bridgedb xml format
regExDataSourceDelimiter - Variable in class org.bridgedb.file.IDMappingReaderFromDelimitedReader
regExIDDelimiter - Variable in class org.bridgedb.file.IDMappingReaderFromDelimitedReader
register(String, String) - Static method in class org.bridgedb.DataSource: Register a new DataSource with (optional) detailed information.
register(String, Driver) - Static method in class org.bridgedb.BridgeDb: Used by Driver implementations to register themselves and make themselves available to the world.
registerAlias(String) - Method in class org.bridgedb.DataSource
registerPattern(DataSource, Pattern) - Static method in class org.bridgedb.DataSourcePatterns: Register a regex Pattern for recognizing a DataSource.
removeIDMapper(IDMapper) - Method in class org.bridgedb.IDMapperStack: Remove an idMapper from the stack.

S

setDataSourceDelimiters(char[]) - Method in class org.bridgedb.file.IDMapperText: Set delimiters between data sources.
setDataSourceDelimiters(char[]) - Method in class org.bridgedb.file.IDMappingReaderFromText: Set delimiters between data sources.
setDataSources(List<DataSource>) - Method in class org.bridgedb.file.IDMappingReaderFromDelimitedReader: Set DataSources.
setIDDelimiters(char[]) - Method in class org.bridgedb.file.IDMapperText: Set delimiters between data IDs.
setIDDelimiters(char[]) - Method in class org.bridgedb.file.IDMappingReaderFromText: Set delimiters between data IDs.
setTransitive(boolean) - Method in class org.bridgedb.IDMapperStack: Set Transitivity mode, where all mappings are combined to infer second degree mappings.
setTransitivity(boolean) - Method in class org.bridgedb.file.IDMapperText: Set transitivity support.
setTransitivity(boolean) - Method in class org.bridgedb.file.IDMappingReaderFromDelimitedReader: Set transitivity support.
strs2regex(char[]) - Static method in class org.bridgedb.file.IDMappingReaderFromText
systemCodeExists(String) - Static method in class org.bridgedb.DataSource: Check if a DataSource with this systemCode has been registered

T

toString() - Method in class org.bridgedb.DataSource: The string representation of a DataSource is equal to it's full name.
toString() - Method in class org.bridgedb.file.IDMapperText
toString() - Method in class org.bridgedb.IDMapperStack
toString() - Method in class org.bridgedb.Xref: This string representation is not meant to be stored or parsed, it is there mostly for debugging purposes.
TransitiveGraph - Class in org.bridgedb.impl: Helper for calculating paths in IDMapperStack in transitive mode.
TransitiveGraph(List<IDMapper>) - Constructor for class org.bridgedb.impl.TransitiveGraph: Constructor: immediately starts calculating paths.
type(String) - Method in class org.bridgedb.DataSource.Builder: Since version 2 This method no longer allow changing the type of a DataSource once set.

U

UNKOWN - Static variable in class org.bridgedb.DataSource
url - Variable in class org.bridgedb.file.IDMappingReaderFromText
urlPattern(String) - Method in class org.bridgedb.DataSource.Builder
urlPatternKnown() - Method in class org.bridgedb.DataSource: Check if a Url pattern is know for this DataSource.
urnBase(String) - Method in class org.bridgedb.DataSource.Builder: This adds a miriam base to the DataSource.

X

Xref - Class in org.bridgedb: Stores an id + DataSource combination, which represents an unique gene product.
Xref(String, DataSource) - Constructor for class org.bridgedb.Xref
Xref(String, DataSource, boolean) - Constructor for class org.bridgedb.Xref
xrefExists(Xref) - Method in class org.bridgedb.file.IDMapperFile: Check whether an Xref is known by the given mapping source.
xrefExists(Xref) - Method in interface org.bridgedb.IDMapper: Check whether an Xref is known by the given mapping source.
xrefExists(Xref) - Method in class org.bridgedb.IDMapperStack: Check whether an Xref is known by the given mapping source.
XrefIterator - Interface in org.bridgedb

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