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

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

BridgeDb - Class in org.bridgedb

Central access point for connecting to IDMappers.

buildsystem - package buildsystem

C

cap - Variable in class org.bridgedb.file.IDMapperFile

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.

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.

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, String) - Method in interface org.bridgedb.AttributeMapper

Get attributes for an entity, such as gene Symbol.

getAttributes(Xref) - Method in interface org.bridgedb.AttributeMapper

Get all attributes for an entity.

getAttributes(Xref, String) - Method in class org.bridgedb.IDMapperStack

Get attributes for an entity, such as gene Symbol.

getAttributes(Xref) - Method in class org.bridgedb.IDMapperStack

Get all attributes for an entity.

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

getByAlias(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

getCompactIdentifier(String) - Method in class org.bridgedb.DataSource

Creates a compact identifier.

getCompactidentifier() - Method in class org.bridgedb.Xref

Uses DataSource.getCompactidentifier() to create a compact identifier, such as uniprot:P12345.

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

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.

getIterator(DataSource) - Method in interface org.bridgedb.XrefIterator

Create an iterator that iterates over all Xrefs of a certain DataSource defined by this IDMapper.

getIterator() - Method in interface org.bridgedb.XrefIterator

Create an iterator that iterates over all Xrefs defined by this IDMapper.

getKeys() - Method in class org.bridgedb.AbstractIDMapperCapabilities

getKeys() - Method in interface org.bridgedb.IDMapperCapabilities

getKnownUrl(String) - Method in class org.bridgedb.DataSource

Turn id into url pointing to info page on the web, e.g.

getKnownUrl() - Method in class org.bridgedb.Xref

Uses DataSource.getKnownUrl to create a valid URL for an online webpage describing this entity.

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(String) - Method in class org.bridgedb.DataSource

Creates a global identifier.

getMiriamURN() - Method in class org.bridgedb.Xref

Uses DataSource.getMiriamURN() to create a global identifier, such as urn:miriam:uniprot:P12345.

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.

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

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(Throwable) - Constructor for exception org.bridgedb.IDMapperException

See Exception(Throwable).

IDMapperException(String, Throwable) - Constructor for exception org.bridgedb.IDMapperException

See Exception(String, Throwable).

IDMapperException(String) - Constructor for exception org.bridgedb.IDMapperException

See Exception (String).

IDMapperException() - Constructor for exception org.bridgedb.IDMapperException

See Exception ().

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.

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(Xref, DataSource...) - Method in class org.bridgedb.AbstractIDMapper

Default implementation of mapID.

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(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(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(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(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.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

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.

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.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, Driver) - Static method in class org.bridgedb.BridgeDb

Used by Driver implementations to register themselves and make themselves available to the world.

register(String, String) - Static method in class org.bridgedb.DataSource

Register a new DataSource with (optional) detailed information.

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 DataSoucre 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

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

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