org.bridgedb

Interface IDMapper

All Known Implementing Classes:

AbstractIDMapper, IDMapperFile, IDMapperStack, IDMapperText, IDMapperWebservice

public interface IDMapper

Base interface for all id mapping methods. Has methods for basic functionality such as looking up cross-references and backpage text.

Method Summary

Modifier and Type	Method and Description
void	close() dispose any resources (such as open database connections) associated with this IDMapper.
Set<Xref>	freeSearch(String text, int limit) free text search for matching symbols or identifiers.
IDMapperCapabilities	getCapabilities()
boolean	isConnected() Use this method to check if the IDMapper is still valid.
Map<Xref,Set<Xref>>	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>	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.
boolean	xrefExists(Xref xref) Check whether an Xref is known by the given mapping source.

Method Detail

mapID

Map<Xref,Set<Xref>> mapID(Collection<Xref> srcXrefs,
                          DataSource... tgtDataSources)
                   throws IDMapperException

Get all cross-references for a set of entities, restricting the result to contain only references from the given set of data sources. Supports one-to-one mapping and one-to-many mapping.

Parameters:

srcXrefs - source Xref, containing ID and ID type/data source

tgtDataSources - target ID types/data sources. Set this to null if you want to retrieve all results.

Returns:

a map from source Xref to target Xref's. The map is not guaranteed to contain a result for each srcXrefs you pass in. This method will never return null however.

Throws:

IDMapperException - if the mapping service is (temporarily) unavailable

mapID

Set<Xref> mapID(Xref ref,
                DataSource... tgtDataSources)
         throws IDMapperException

Get all cross-references for the given entity, restricting the result to contain only references from the given set of data sources.

Parameters:

ref - the entity to get cross-references for.

tgtDataSources - target ID types/data sources. Set this to null if you want to retrieve all results.

Returns:

A Set containing the cross references, or an empty Set when no cross references could be found. This method does not return null.

Throws:

IDMapperException - if the mapping service is (temporarily) unavailable

xrefExists

boolean xrefExists(Xref xref)
            throws IDMapperException

Check whether an Xref is known by the given mapping source. This is an optionally supported operation.

Parameters:

xref - reference to check

Returns:

if the reference exists, false if not

Throws:

IDMapperException - if failed, UnsupportedOperationException if it's not supported by the Driver.

freeSearch

Set<Xref> freeSearch(String text,
                     int limit)
              throws IDMapperException

free text search for matching symbols or identifiers.

Parameters:

text - text to search

limit - up limit of number of hits

Returns:

a set of hit references

Throws:

IDMapperException - if failed

getCapabilities

IDMapperCapabilities getCapabilities()

Returns:

capacities of the ID mapper

close

void close()
    throws IDMapperException

dispose any resources (such as open database connections) associated with this IDMapper.

Throws:

IDMapperException - if the associated resources could not be freed.

isConnected

boolean isConnected()

Use this method to check if the IDMapper is still valid.

Returns:

false after the close() method is called on this object, true otherwise