org.bridgedb.file

Class IDMapperFile

java.lang.Object

org.bridgedb.file.IDMapperFile

All Implemented Interfaces:

IDMapper

Direct Known Subclasses:

IDMapperText

public abstract class IDMapperFile
extends Object
implements IDMapper

Interface for ID mapping from files.

Field Summary

Fields

Modifier and Type	Field and Description
protected org.bridgedb.file.IDMapperFile.IDMapperFileCapabilities	cap
protected IDMappingReader	reader

Constructor Summary

Constructors

Constructor and Description
IDMapperFile(IDMappingReader reader) Constructor from a IDMappingReader.
IDMapperFile(IDMappingReader reader, boolean freeSearch) Constructor from a IDMappingReader and user-defined free search capacity.

Method Summary

Modifier and Type	Method and Description
void	close() dispose any resources (such as open database connections) associated with this IDMapper.
IDMapperCapabilities	getCapabilities()
protected IDMappingReader	getIDMappingReader()
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 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	xrefExists(Xref xref) Check whether an Xref is known by the given mapping source.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.bridgedb.IDMapper

freeSearch

Field Detail

cap

protected final org.bridgedb.file.IDMapperFile.IDMapperFileCapabilities cap

reader

protected final IDMappingReader reader

Constructor Detail

IDMapperFile

public IDMapperFile(IDMappingReader reader)
             throws IDMapperException

Constructor from a IDMappingReader. transitivity is unsupported by default.

Parameters:

reader - ID mapping reader

Throws:

IDMapperException - when failed to read

IDMapperFile

public IDMapperFile(IDMappingReader reader,
                    boolean freeSearch)
             throws IDMapperException

Constructor from a IDMappingReader and user-defined free search capacity.

Parameters:

reader - ID mapping reader

freeSearch - if this IDMapper supports free search

Throws:

IDMapperException - when failed to read

IllegalArgumentException - if reader is null

Method Detail

mapID

public 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.

Specified by:

mapID in interface IDMapper

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

public Set<Xref> mapID(Xref srcXref,
                       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.

Specified by:

mapID in interface IDMapper

Parameters:

srcXref - 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

public boolean xrefExists(Xref xref)
                   throws IDMapperException

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

Specified by:

xrefExists in interface IDMapper

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.

close

public void close()
           throws IDMapperException

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

Specified by:

close in interface IDMapper

Throws:

IDMapperException - if the associated resources could not be freed.

isConnected

public boolean isConnected()

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

Specified by:

isConnected in interface IDMapper

Returns:

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

getCapabilities

public IDMapperCapabilities getCapabilities()

Specified by:

getCapabilities in interface IDMapper

Returns:

capacities of the ID mapper

getIDMappingReader

protected IDMappingReader getIDMappingReader()