Package de.julielab.genemapper

Class GeneMapper

java.lang.Object

de.julielab.genemapper.GeneMapper

public class GeneMapper
extends Object

Field Summary

Fields

Modifier and Type	Field	Description
static String	APP_NAME
static boolean	LEGACY_INDEX_SUPPORT
static boolean	TEST_MODE

Constructor Summary

Constructors

Constructor	Description
GeneMapper(Configuration config, MappingCore mappingCore)

Method Summary

Modifier and Type	Method	Description
void	clearLexicalRankingModel()
void	clearSemanticRankingModel()
Configuration	getConfiguration()
MappingCore	getMappingCore()
de.julielab.geneexpbase.genemodel.DocumentMappingResult	map(de.julielab.geneexpbase.genemodel.GeneDocument document)
de.julielab.geneexpbase.genemodel.DocumentMappingResult	map(de.julielab.geneexpbase.genemodel.GeneDocument doc, de.julielab.geneexpbase.configuration.Parameters parameterMap)
de.julielab.geneexpbase.genemodel.DocumentMappingResult	map(de.julielab.geneexpbase.genemodel.GeneDocument document, de.julielab.geneexpbase.configuration.Parameters parameterMap, Stats stats)
de.julielab.geneexpbase.genemodel.DocumentMappingResult	map(de.julielab.geneexpbase.genemodel.GeneDocument document, Stats stats)
de.julielab.geneexpbase.genemodel.MentionMappingResult	map(de.julielab.geneexpbase.genemodel.GeneMention searchTerm, org.apache.lucene.search.BooleanQuery contextQuery, String documentContext)	Actual mapping method.
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	map(String searchTerm, org.apache.lucene.search.BooleanQuery contextQuery)	A wrapper to the main mapping function.
de.julielab.geneexpbase.genemodel.MentionMappingResult	map(String term, org.apache.lucene.search.BooleanQuery contextQuery, String documentContext)	Convenience method mostly used for tests.
ArrayList<de.julielab.geneexpbase.candidateretrieval.SynHit>	mapTopN(String searchTerm, int topN)	This mapping returns a list of SynHits.
void	setMappingCore(MappingCore mappingCore)

Methods inherited from class java.lang.Object

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

Field Detail

APP_NAME

public static final String APP_NAME

See Also:

Constant Field Values

LEGACY_INDEX_SUPPORT

public static final boolean LEGACY_INDEX_SUPPORT

See Also:

Constant Field Values

TEST_MODE

public static boolean TEST_MODE

Constructor Detail

GeneMapper

@Inject
public GeneMapper(Configuration config,
                  MappingCore mappingCore)

Method Detail

map

public List<de.julielab.geneexpbase.candidateretrieval.SynHit> map(String searchTerm,
                                                                   org.apache.lucene.search.BooleanQuery contextQuery)
                                                            throws GeneMapperException

A wrapper to the main mapping function. This one does not require an organism to be specified and does thus completely organism-agnostic search (currently used basically for backward compatibility to BC evaluation).

Parameters:

searchTerm -

contextQuery -

Returns:

the SynHits that apply to the given searchTerm

Throws:

Exception

GeneMapperException

map

public de.julielab.geneexpbase.genemodel.MentionMappingResult map(de.julielab.geneexpbase.genemodel.GeneMention searchTerm,
                                                                  org.apache.lucene.search.BooleanQuery contextQuery,
                                                                  String documentContext)
                                                           throws GeneMapperException

Actual mapping method. This mapping functions has semantic disambiguation as well. First it checks for general, organism-specific hits (getCandidates). If organisms is given (i.e. is not null or not empty) semantic disambiguation is performed with this organism list.

Parameters:

searchTerm - the term to do the mapping for

contextQuery - the term's context (i.e. the document/abstract where it was found in)

documentContext -

Returns:

ArrayList with SynHits

Throws:

Exception

GeneMapperException

map

public de.julielab.geneexpbase.genemodel.DocumentMappingResult map(de.julielab.geneexpbase.genemodel.GeneDocument document)
                                                            throws GeneMapperException

Throws:

GeneMapperException

mapTopN

public ArrayList<de.julielab.geneexpbase.candidateretrieval.SynHit> mapTopN(String searchTerm,
                                                                            int topN)
                                                                     throws IOException,
                                                                            de.julielab.geneexpbase.candidateretrieval.GeneCandidateRetrievalException

This mapping returns a list of SynHits. No semantic disambiguation is done here. TopN hits with the highest (lucene) scores are returned. Not needed for actual mapping but used for generating training material for MaxEntScorer.

Parameters:

searchTerm - the term to be mapped

topN - number of hits to be returned

Throws:

de.julielab.geneexpbase.candidateretrieval.GeneCandidateRetrievalException

IOException

getMappingCore

public MappingCore getMappingCore()

setMappingCore

public void setMappingCore(MappingCore mappingCore)

map

public de.julielab.geneexpbase.genemodel.MentionMappingResult map(String term,
                                                                  org.apache.lucene.search.BooleanQuery contextQuery,
                                                                  String documentContext)
                                                           throws GeneMapperException

Convenience method mostly used for tests. The term will be wrapped into a GeneMention. However, no offset information or other data about the original gene mention will be known, of course.

Parameters:

term -

contextQuery -

documentContext -

Returns:

Throws:

Exception

GeneMapperException

getConfiguration

public Configuration getConfiguration()

map

public de.julielab.geneexpbase.genemodel.DocumentMappingResult map(de.julielab.geneexpbase.genemodel.GeneDocument document,
                                                                   Stats stats)
                                                            throws GeneMapperException

Throws:

GeneMapperException

map

public de.julielab.geneexpbase.genemodel.DocumentMappingResult map(de.julielab.geneexpbase.genemodel.GeneDocument document,
                                                                   de.julielab.geneexpbase.configuration.Parameters parameterMap,
                                                                   Stats stats)
                                                            throws GeneMapperException

Throws:

GeneMapperException

map

public de.julielab.geneexpbase.genemodel.DocumentMappingResult map(de.julielab.geneexpbase.genemodel.GeneDocument doc,
                                                                   de.julielab.geneexpbase.configuration.Parameters parameterMap)
                                                            throws GeneMapperException

Throws:

GeneMapperException

clearLexicalRankingModel

public void clearLexicalRankingModel()

clearSemanticRankingModel

public void clearSemanticRankingModel()