Package ubic.gemma.core.loader.util.mapper

Class RenamingBioAssayMapper

java.lang.Object

ubic.gemma.core.loader.util.mapper.RenamingBioAssayMapper

All Implemented Interfaces:

BioAssayMapper, EntityMapper<BioAssay>

public class RenamingBioAssayMapper
extends Object
implements BioAssayMapper

A BioAssay-to-sample-name matcher that renames samples before matching them.

Author:

poirigui

Nested Class Summary

Nested classes/interfaces inherited from interface ubic.gemma.core.loader.util.mapper.EntityMapper

EntityMapper.MappingStatistics, EntityMapper.StatefulEntityMapper<T extends Identifiable>

Constructor Summary

Constructors

Constructor	Description
RenamingBioAssayMapper(BioAssayMapper delegate, String[] bioAssayNames, String[] sampleNames)

Method Summary

Modifier and Type	Method	Description
boolean	contains(Collection<BioAssay> bioAssays, String sampleName)	Check if any of the candidates can be mapped to the identifier.
boolean	containsAny(Collection<BioAssay> bioAssays, Collection<String> sampleNames)	Check if any of the candidates can be mapped to any of the identifiers.
EntityMapper.StatefulEntityMapper<BioAssay>	forCandidates(Collection<BioAssay> candidates)	Create a stateful mapper for a set of candidates.
String	getName()	Obtain the name of the mapping strategy.
Set<BioAssay>	matchAll(Collection<BioAssay> bioAssays, String sampleName)	Match the identifier to all the candidates.
Optional<BioAssay>	matchOne(Collection<BioAssay> bioAssays, String sampleName)	Map the identifier to a single candidate.
String	toString()

Methods inherited from class java.lang.Object

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

Methods inherited from interface ubic.gemma.core.loader.util.mapper.BioAssayMapper

forCandidates

Methods inherited from interface ubic.gemma.core.loader.util.mapper.EntityMapper

getMappingStatistics, matchAll, matchOne

Constructor Detail

RenamingBioAssayMapper

public RenamingBioAssayMapper(BioAssayMapper delegate,
                              String[] bioAssayNames,
                              String[] sampleNames)

Parameters:

delegate - a matcher that performs the underlying comparison of BA IDs

bioAssayNames - the BioAssay identifiers to use

sampleNames - the corresponding sample identifiers to use

Method Detail

getName

public String getName()

Description copied from interface: EntityMapper

Obtain the name of the mapping strategy.

Specified by:

getName in interface EntityMapper<BioAssay>

contains

public boolean contains(Collection<BioAssay> bioAssays,
                        String sampleName)

Description copied from interface: EntityMapper

Check if any of the candidates can be mapped to the identifier.

Specified by:

contains in interface EntityMapper<BioAssay>

containsAny

public boolean containsAny(Collection<BioAssay> bioAssays,
                           Collection<String> sampleNames)

Description copied from interface: EntityMapper

Check if any of the candidates can be mapped to any of the identifiers.

Specified by:

containsAny in interface EntityMapper<BioAssay>

matchOne

public Optional<BioAssay> matchOne(Collection<BioAssay> bioAssays,
                                   String sampleName)

Description copied from interface: EntityMapper

Map the identifier to a single candidate.

If more than one candidate matches the identifier, Optional.empty() is returned.

Specified by:

matchOne in interface EntityMapper<BioAssay>

matchAll

public Set<BioAssay> matchAll(Collection<BioAssay> bioAssays,
                              String sampleName)

Description copied from interface: EntityMapper

Match the identifier to all the candidates.

Specified by:

matchAll in interface EntityMapper<BioAssay>

toString

public String toString()

Overrides:

toString in class Object

forCandidates

public EntityMapper.StatefulEntityMapper<BioAssay> forCandidates(Collection<BioAssay> candidates)

Description copied from interface: EntityMapper

Create a stateful mapper for a set of candidates.

Specified by:

forCandidates in interface EntityMapper<BioAssay>