Package de.julielab.jules.ae.genemapping

Interface CandidateRetrieval

All Known Implementing Classes:

LuceneCandidateRetrieval

public interface CandidateRetrieval

Method Summary

Modifier and Type	Method	Description
java.util.List<SynHit>	getCandidates(GeneMention geneMention)
java.util.List<SynHit>	getCandidates(GeneMention geneMention, java.lang.String organism)
java.util.List<SynHit>	getCandidates(GeneMention geneMention, java.util.Collection<java.lang.String> organisms)
java.util.List<SynHit>	getCandidates(java.lang.String originalSearchTerm)
java.util.List<SynHit>	getCandidates(java.lang.String geneMentionText, java.lang.String organism)
java.util.List<SynHit>	getCandidates(java.lang.String geneMentionText, java.util.Collection<java.lang.String> organism)
java.util.List<SynHit>	getIndexEntries(java.util.List<java.lang.String> ids)	Retrieves the first index hit for each ID.
java.util.List<java.lang.String>	getSynonyms(java.lang.String id)
java.lang.String	mapGeneIdToTaxId(java.lang.String geneId)

Method Detail

getCandidates

java.util.List<SynHit> getCandidates(java.lang.String originalSearchTerm)
                              throws GeneCandidateRetrievalException

Throws:

GeneCandidateRetrievalException

getCandidates

java.util.List<SynHit> getCandidates(GeneMention geneMention)
                              throws GeneCandidateRetrievalException

Throws:

GeneCandidateRetrievalException

getCandidates

java.util.List<SynHit> getCandidates(GeneMention geneMention,
                                     java.lang.String organism)
                              throws GeneCandidateRetrievalException

Throws:

GeneCandidateRetrievalException

getCandidates

java.util.List<SynHit> getCandidates(GeneMention geneMention,
                                     java.util.Collection<java.lang.String> organisms)
                              throws GeneCandidateRetrievalException

Throws:

GeneCandidateRetrievalException

getCandidates

java.util.List<SynHit> getCandidates(java.lang.String geneMentionText,
                                     java.lang.String organism)
                              throws GeneCandidateRetrievalException

Throws:

GeneCandidateRetrievalException

getCandidates

java.util.List<SynHit> getCandidates(java.lang.String geneMentionText,
                                     java.util.Collection<java.lang.String> organism)
                              throws GeneCandidateRetrievalException

Throws:

GeneCandidateRetrievalException

mapGeneIdToTaxId

java.lang.String mapGeneIdToTaxId(java.lang.String geneId)
                           throws java.io.IOException

Throws:

java.io.IOException

getIndexEntries

java.util.List<SynHit> getIndexEntries(java.util.List<java.lang.String> ids)
                                throws java.io.IOException

Retrieves the first index hit for each ID.

Parameters:

ids - The gene IDs for which to retrieve a single index hit.

Returns:

One index entry - or null - for each input ID.

Throws:

java.io.IOException - If there is an issue reading the index.

getSynonyms

java.util.List<java.lang.String> getSynonyms(java.lang.String id)
                                      throws java.io.IOException

Throws:

java.io.IOException