/**
* Given an accession, try and infer which resource the identifier is from. If the accession is
* very general and can not be inferred it is added to the {@link #ambiguous()} set. If a single
* resource was inferred it will try to be mapped to any entities matching the given key.
*
* <blockquote>
*
* <pre>
* IdentifierMap mapper = ...;
* mapper.map("atp", "C00002");
* mapper.map("atp", "CHEBI:57299");
* </pre>
*
* </blockquote>
*
* @param key the key to locate the entity
* @param accession the accession to infer a resource from
* @return an entity <i>handled</i> the identifier
* @see #ambiguous()
*/
public boolean map(K key, String accession) {
Collection<Class<? extends Identifier>> ids = idFactory.ofPattern(accession);
if (ids.size() == 1) {
Identifier identifier = idFactory.ofClass(ids.iterator().next());
identifier.setAccession(accession);
return map(key, identifier);
} else if (ids.size() > 1) {
ambiguous.add(accession);
}
return false;
}
/**
* Find the identifier for the resource name and set the accession and add then try to map the
* identifier to an entity which matches the key. If the name cannot be found it is added to
* {@link #unknown()}. If the identifier is invalid is will be added to {@link #invalid()}.
*
* <blockquote>
*
* <pre>
* IdentifierMap mapper = ...;
* mapper.map("atp", "C00002", "KEGG Compound");
* mapper.map("atp", "CHEBI:57299", "ChEBI");
* </pre>
*
* </blockquote>
*
* @param key look up entities
* @param accession identifier accession
* @param name resource name
* @return an entity <i>handled</i> the identifier
* @see #invalid()
* @see #unknown()
*/
public boolean map(K key, String accession, String name) {
Identifier identifier = idFactory.ofName(name);
if (identifier != IdentifierFactory.EMPTY_IDENTIFIER) {
identifier.setAccession(accession);
if (identifier.isValid()) {
return map(key, identifier);
} else {
invalid.add(accession);
}
} else {
unknown.add(name);
}
return false;
}
