Package de.julielab.genemapper.disambig

Class SemanticContextIndex

java.lang.Object

de.julielab.genemapper.disambig.SemanticContextIndex

All Implemented Interfaces:

SemanticIndex

public class SemanticContextIndex
extends Object
implements SemanticIndex

Field Summary

Fields

Modifier and Type	Field	Description
org.apache.lucene.search.IndexSearcher	searcher

Constructor Summary

Constructors

Constructor	Description
SemanticContextIndex(File indexDir)

Method Summary

Modifier and Type	Method	Description
de.julielab.geneexpbase.candidateretrieval.SynHit	doDisambiguation(List<de.julielab.geneexpbase.candidateretrieval.SynHit> filteredCandidates, org.apache.lucene.search.Query query)	does semantic disambiguation, takes best one
de.julielab.geneexpbase.candidateretrieval.SynHit	doDisambiguation(List<de.julielab.geneexpbase.candidateretrieval.SynHit> filteredCandidates, org.apache.lucene.search.Query query, double minContextScore)	does semantic disambiguation, takes best one if its semantic score is above or equals minScore threshold
de.julielab.geneexpbase.candidateretrieval.SynHit	doSeparateDisambiguation(ArrayList<de.julielab.geneexpbase.candidateretrieval.SynHit> disambigList, String context, double minContextScore)	does semantic disambiguation on each SynHit separately, takes best one if its semantic score is above or equals minScore threshold
org.apache.lucene.search.TopDocs	getContextForSynHits(List<de.julielab.geneexpbase.candidateretrieval.SynHit> hits, Map<String,de.julielab.geneexpbase.candidateretrieval.SynHit> id2Hit, org.apache.lucene.search.Query query)
org.apache.lucene.search.IndexSearcher	getSemanticIndexSearcher()
org.apache.lucene.search.BooleanQuery	makeContextQuery(String context)
org.apache.lucene.search.Query	makeQuery(String[] allowedIDs, org.apache.lucene.search.Query query)
org.apache.lucene.search.BooleanQuery	makeQuery(String allowedID, org.apache.lucene.search.BooleanQuery contextQuery)
org.apache.lucene.search.BooleanQuery	makeSeparateQuery(String id, String context)	generates a boolean query from the context and a single ids: the id has to match and the context is combined by OR.
Map<String,String>	retrieveGeneContexts(List<de.julielab.geneexpbase.candidateretrieval.SynHit> candidates)

Methods inherited from class java.lang.Object

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

Field Detail

searcher

public org.apache.lucene.search.IndexSearcher searcher

Constructor Detail

SemanticContextIndex

public SemanticContextIndex(File indexDir)
                     throws IOException

Throws:

IOException

Method Detail

doDisambiguation

public de.julielab.geneexpbase.candidateretrieval.SynHit doDisambiguation(List<de.julielab.geneexpbase.candidateretrieval.SynHit> filteredCandidates,
                                                                          org.apache.lucene.search.Query query)
                                                                   throws IOException

does semantic disambiguation, takes best one

Throws:

IOException

doDisambiguation

public de.julielab.geneexpbase.candidateretrieval.SynHit doDisambiguation(List<de.julielab.geneexpbase.candidateretrieval.SynHit> filteredCandidates,
                                                                          org.apache.lucene.search.Query query,
                                                                          double minContextScore)
                                                                   throws IOException

does semantic disambiguation, takes best one if its semantic score is above or equals minScore threshold

Throws:

IOException

retrieveGeneContexts

public Map<String,String> retrieveGeneContexts(List<de.julielab.geneexpbase.candidateretrieval.SynHit> candidates)
                                              throws IOException

Throws:

IOException

getContextForSynHits

public org.apache.lucene.search.TopDocs getContextForSynHits(List<de.julielab.geneexpbase.candidateretrieval.SynHit> hits,
                                                             Map<String,de.julielab.geneexpbase.candidateretrieval.SynHit> id2Hit,
                                                             org.apache.lucene.search.Query query)
                                                      throws IOException

Throws:

IOException

makeContextQuery

public org.apache.lucene.search.BooleanQuery makeContextQuery(String context)
                                                       throws IOException

Throws:

IOException

makeQuery

public org.apache.lucene.search.Query makeQuery(String[] allowedIDs,
                                                org.apache.lucene.search.Query query)
                                         throws IOException

Throws:

IOException

makeQuery

public org.apache.lucene.search.BooleanQuery makeQuery(String allowedID,
                                                       org.apache.lucene.search.BooleanQuery contextQuery)
                                                throws IOException

Parameters:

allowedID - -- only one id is passed

contextQuery - -- the context query

Returns:

BooleanQuery

Throws:

IOException

doSeparateDisambiguation

public de.julielab.geneexpbase.candidateretrieval.SynHit doSeparateDisambiguation(ArrayList<de.julielab.geneexpbase.candidateretrieval.SynHit> disambigList,
                                                                                  String context,
                                                                                  double minContextScore)
                                                                           throws IOException

does semantic disambiguation on each SynHit separately, takes best one if its semantic score is above or equals minScore threshold

Throws:

IOException

makeSeparateQuery

public org.apache.lucene.search.BooleanQuery makeSeparateQuery(String id,
                                                               String context)
                                                        throws IOException

generates a boolean query from the context and a single ids: the id has to match and the context is combined by OR.

TODO requires testing!

Throws:

IOException

getSemanticIndexSearcher

public org.apache.lucene.search.IndexSearcher getSemanticIndexSearcher()