A B C D E F G H I K L M N O P R S T U V W X Z

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

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.

AFFY - Static variable in class org.bridgedb.bio.BioDataSource

AGILENT - Static variable in class org.bridgedb.bio.BioDataSource

asDataSource() - Method in class org.bridgedb.DataSource.Builder

AttributeMapper - Interface in org.bridgedb

AttributeMapper knows about attributes for Xrefs.

B

BIOCYC - Static variable in class org.bridgedb.bio.BioDataSource

BioDataSource - Class in org.bridgedb.bio

Definition of many common biological DataSources.

BioDataSource() - Constructor for class org.bridgedb.bio.BioDataSource

BIOGRID - Static variable in class org.bridgedb.bio.BioDataSource

BridgeDb - Class in org.bridgedb

Central access point for connecting to IDMappers.

C

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

CAS - Static variable in class org.bridgedb.bio.BioDataSource

CCDS - Static variable in class org.bridgedb.bio.BioDataSource

CHEBI - Static variable in class org.bridgedb.bio.BioDataSource

CHEMSPIDER - Static variable in class org.bridgedb.bio.BioDataSource

CINT - Static variable in class org.bridgedb.bio.BioDataSource

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.

code() - Method in enum org.bridgedb.bio.Organism

CODELINK - Static variable in class org.bridgedb.bio.BioDataSource

codes() - Static method in enum org.bridgedb.bio.Organism

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, such as It's full name ("Ensembl") It's system code ("En") It's main url ("http://www.ensembl.org") Id-specific url's ("http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=" + id) The DataSource class uses the extensible enum pattern.

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.

Driver - Interface in org.bridgedb

A Driver knows how to create an IDMapper instance.

dsValid - Variable in class org.bridgedb.file.IDMappingReaderFromDelimitedReader

E

ECOLI - Static variable in class org.bridgedb.bio.BioDataSource

EMBL - Static variable in class org.bridgedb.bio.BioDataSource

ENSEMBL - Static variable in class org.bridgedb.bio.BioDataSource

Deprecated. use one of the organism-specific system codes instead

ENSEMBL_BSUBTILIS - Static variable in class org.bridgedb.bio.BioDataSource

ENSEMBL_CELEGANS - Static variable in class org.bridgedb.bio.BioDataSource

ENSEMBL_CHICKEN - Static variable in class org.bridgedb.bio.BioDataSource

ENSEMBL_CHIMP - Static variable in class org.bridgedb.bio.BioDataSource

ENSEMBL_COW - Static variable in class org.bridgedb.bio.BioDataSource

ENSEMBL_DOG - Static variable in class org.bridgedb.bio.BioDataSource

ENSEMBL_ECOLI - Static variable in class org.bridgedb.bio.BioDataSource

ENSEMBL_FRUITFLY - Static variable in class org.bridgedb.bio.BioDataSource

ENSEMBL_HORSE - Static variable in class org.bridgedb.bio.BioDataSource

ENSEMBL_HUMAN - Static variable in class org.bridgedb.bio.BioDataSource

ENSEMBL_MOSQUITO - Static variable in class org.bridgedb.bio.BioDataSource

ENSEMBL_MOUSE - Static variable in class org.bridgedb.bio.BioDataSource

ENSEMBL_MTUBERCULOSIS - Static variable in class org.bridgedb.bio.BioDataSource

ENSEMBL_RAT - Static variable in class org.bridgedb.bio.BioDataSource

ENSEMBL_SCEREVISIAE - Static variable in class org.bridgedb.bio.BioDataSource

ENSEMBL_XENOPUS - Static variable in class org.bridgedb.bio.BioDataSource

ENSEMBL_ZEBRAFISH - Static variable in class org.bridgedb.bio.BioDataSource

ENTREZ_GENE - Static variable in class org.bridgedb.bio.BioDataSource

ENZYME_CODE - Static variable in class org.bridgedb.bio.BioDataSource

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

F

FLYBASE - Static variable in class org.bridgedb.bio.BioDataSource

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.

fromCode(String) - Static method in enum org.bridgedb.bio.Organism

fromLatinName(String) - Static method in enum org.bridgedb.bio.Organism

fromShortName(String) - Static method in enum org.bridgedb.bio.Organism

fromUrn(String) - Static method in class org.bridgedb.Xref

G

GENBANK - Static variable in class org.bridgedb.bio.BioDataSource

GENE_ONTOLOGY - Static variable in class org.bridgedb.bio.BioDataSource

GENE_WIKI - Static variable in class org.bridgedb.bio.BioDataSource

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.

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

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

returns pre-existing DataSource object by full name, if it exists, or creates a new one.

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

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

getCapabilities() - Method in class org.bridgedb.file.IDMapperFile

getCapabilities() - Method in interface org.bridgedb.IDMapper

getCapabilities() - Method in class org.bridgedb.IDMapperStack

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.

getExample() - 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

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.

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

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

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

getSpeciesSpecificEnsembl(Organism) - Static method in class org.bridgedb.bio.BioDataSource

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

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

getURL() - Method in class org.bridgedb.file.IDMapperText

Get URL of the file.

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

Uses DataSource.getUrl() to create a valid URL for an online webpage describing this entity.

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

Creates a global identifier.

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

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

GRAMENE_ARABIDOPSIS - Static variable in class org.bridgedb.bio.BioDataSource

GRAMENE_GENES_DB - Static variable in class org.bridgedb.bio.BioDataSource

GRAMENE_LITERATURE - Static variable in class org.bridgedb.bio.BioDataSource

GRAMENE_PATHWAY - Static variable in class org.bridgedb.bio.BioDataSource

GRAMENE_RICE - Static variable in class org.bridgedb.bio.BioDataSource

H

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

hashCode calculated from id and datasource combined.

HMDB - Static variable in class org.bridgedb.bio.BioDataSource

HSGENE - Static variable in class org.bridgedb.bio.BioDataSource

HUGO - Static variable in class org.bridgedb.bio.BioDataSource

I

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

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

Constuctor from a IDMappingReader.

IDMapperFile(IDMappingReader, boolean) - Constructor for class org.bridgedb.file.IDMapperFile

Constuctor 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

ILLUMINA - Static variable in class org.bridgedb.bio.BioDataSource

init() - Static method in class org.bridgedb.bio.BioDataSource

Call this to initialize the BioDataSource.XXX constants.

INTERPRO - Static variable in class org.bridgedb.bio.BioDataSource

IPI - Static variable in class org.bridgedb.bio.BioDataSource

IRGSP_GENE - Static variable in class org.bridgedb.bio.BioDataSource

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

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

K

KEGG_COMPOUND - Static variable in class org.bridgedb.bio.BioDataSource

KEGG_GENES - Static variable in class org.bridgedb.bio.BioDataSource

L

latinName() - Method in enum org.bridgedb.bio.Organism

latinNames() - Static method in enum org.bridgedb.bio.Organism

latinNamesArray() - Static method in enum org.bridgedb.bio.Organism

M

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

MAIZE_GDB - Static variable in class org.bridgedb.bio.BioDataSource

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.

MATCH_ID - Static variable in interface org.bridgedb.AttributeMapper

use this magic constant as the attrType parameter to also search for identifiers.

MGI - Static variable in class org.bridgedb.bio.BioDataSource

MIRBASE - Static variable in class org.bridgedb.bio.BioDataSource

N

NASC_GENE - Static variable in class org.bridgedb.bio.BioDataSource

NUGOWIKI - Static variable in class org.bridgedb.bio.BioDataSource

O

OMIM - Static variable in class org.bridgedb.bio.BioDataSource

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.bio - package org.bridgedb.bio

Contains DataSource definitions for many common biological databases, and id patterns for guessing data sources.

org.bridgedb.file - package org.bridgedb.file

Driver and helper classes for using simple files as an identifier mapping service.

org.bridgedb.webservice - package org.bridgedb.webservice

Organism - Enum in org.bridgedb.bio

enum representing organisms understood by PathVisio.

organism(Object) - Method in class org.bridgedb.DataSource.Builder

ORYZA_BASE - Static variable in class org.bridgedb.bio.BioDataSource

OTHER - Static variable in class org.bridgedb.bio.BioDataSource

P

PDB - Static variable in class org.bridgedb.bio.BioDataSource

PFAM - Static variable in class org.bridgedb.bio.BioDataSource

PLANTGDB - Static variable in class org.bridgedb.bio.BioDataSource

primary(boolean) - Method in class org.bridgedb.DataSource.Builder

PUBCHEM - Static variable in class org.bridgedb.bio.BioDataSource

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.

REFSEQ - Static variable in class org.bridgedb.bio.BioDataSource

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.

RFAM - Static variable in class org.bridgedb.bio.BioDataSource

RGD - Static variable in class org.bridgedb.bio.BioDataSource

RICE_ENSEMBL_GENE - Static variable in class org.bridgedb.bio.BioDataSource

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.

SGD - Static variable in class org.bridgedb.bio.BioDataSource

shortName() - Method in enum org.bridgedb.bio.Organism

SNP - Static variable in class org.bridgedb.bio.BioDataSource

strs2regex(char[]) - Static method in class org.bridgedb.file.IDMappingReaderFromText

T

TAIR - Static variable in class org.bridgedb.bio.BioDataSource

TIGR - Static variable in class org.bridgedb.bio.BioDataSource

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.IDMapperStack

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

TUBERCULIST - Static variable in class org.bridgedb.bio.BioDataSource

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

U

UCSC - Static variable in class org.bridgedb.bio.BioDataSource

UNIGENE - Static variable in class org.bridgedb.bio.BioDataSource

UNIPROT - Static variable in class org.bridgedb.bio.BioDataSource

url - Variable in class org.bridgedb.file.IDMappingReaderFromText

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

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

V

valueOf(String) - Static method in enum org.bridgedb.bio.Organism

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.bridgedb.bio.Organism

Returns an array containing the constants of this enum type, in the order they are declared.

W

WHEAT_GENE_CATALOG - Static variable in class org.bridgedb.bio.BioDataSource

WHEAT_GENE_NAMES - Static variable in class org.bridgedb.bio.BioDataSource

WHEAT_GENE_REFERENCES - Static variable in class org.bridgedb.bio.BioDataSource

WIKIGENE - Static variable in class org.bridgedb.bio.BioDataSource

WIKIPATHWAYS - Static variable in class org.bridgedb.bio.BioDataSource

WIKIPEDIA - Static variable in class org.bridgedb.bio.BioDataSource

WORMBASE - Static variable in class org.bridgedb.bio.BioDataSource

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

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

Z

ZFIN - Static variable in class org.bridgedb.bio.BioDataSource

A B C D E F G H I K L M N O P R S T U V W X Z