Package de.julielab.jules.ae.genemapping

Class GeneMapping

java.lang.Object

de.julielab.jules.ae.genemapping.GeneMapping

public class GeneMapping
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field	Description
static int	JAROWINKLER_SCORER
static boolean	LEGACY_INDEX_SUPPORT
static int	LEVENSHTEIN_SCORER
static int	LUCENE_SCORER
static java.lang.String	MAPPING_CORE	Deprecated.
static int	MAXENT_SCORER
static int	SIMPLE_SCORER
static java.lang.String	SOURCE_DEFINITION
static int	TFIDF	Deprecated.
static int	TOKEN_JAROWINKLER_SCORER

Constructor Summary

Constructors

Constructor	Description
GeneMapping(GeneMappingConfiguration configuration)
GeneMapping(java.io.File propertiesFile)	Main constructor for the GeneMapper reading especially properties information.

Method Summary

Modifier and Type	Method	Description
GeneMappingConfiguration	getConfiguration()
MappingCore	getMappingCore()
DocumentMappingResult	map(GeneDocument document)
MentionMappingResult	map(GeneMention searchTerm, org.apache.lucene.search.BooleanQuery contextQuery, java.lang.String documentContext)	Actual mapping method.
java.util.List<SynHit>	map(java.lang.String searchTerm, org.apache.lucene.search.BooleanQuery contextQuery)	A wrapper to the main mapping function.
MentionMappingResult	map(java.lang.String term, org.apache.lucene.search.BooleanQuery contextQuery, java.lang.String documentContext)	Convenience method mostly used for tests.
java.util.ArrayList<SynHit>	mapTopN(java.lang.String searchTerm, int topN)	This mapping returns a list of SynHits.
static java.lang.String	removeDomainFamilies(java.lang.String normalizedSearchTerm)
static java.lang.String	removeModifiers(java.lang.String normalizedSearchTerm)
static java.lang.String	removeNondescriptives(java.lang.String normalizedSearchTerm)
static java.lang.String	removePremodifiers(java.lang.String normalizedSearchTerm)
static java.lang.String	removeUnspecifieds(java.lang.String normalizedSearchTerm)
void	setMappingCore(MappingCore mappingCore)

Methods inherited from class java.lang.Object

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

Field Detail

LEGACY_INDEX_SUPPORT

public static final boolean LEGACY_INDEX_SUPPORT

See Also:

Constant Field Values

SOURCE_DEFINITION

public static final java.lang.String SOURCE_DEFINITION

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Constant Field Values

SIMPLE_SCORER

public static final int SIMPLE_SCORER

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Constant Field Values

TOKEN_JAROWINKLER_SCORER

public static final int TOKEN_JAROWINKLER_SCORER

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Constant Field Values

MAXENT_SCORER

public static final int MAXENT_SCORER

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Constant Field Values

JAROWINKLER_SCORER

public static final int JAROWINKLER_SCORER

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Constant Field Values

LEVENSHTEIN_SCORER

public static final int LEVENSHTEIN_SCORER

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Constant Field Values

TFIDF

public static final int TFIDF

Deprecated.

This was a test using SecondString TFIDF for scoring but wasn't used eventually. Lucene is very good.

See Also:

Constant Field Values

LUCENE_SCORER

public static final int LUCENE_SCORER

See Also:

Constant Field Values

MAPPING_CORE

@Deprecated
public static final java.lang.String MAPPING_CORE

Deprecated.

See Also:

Constant Field Values

Constructor Detail

GeneMapping

public GeneMapping(java.io.File propertiesFile)
            throws java.io.IOException,
                   GeneMappingException

Main constructor for the GeneMapper reading especially properties information.

Parameters:

propertiesFile -

Throws:

java.io.IOException

GeneMappingException

org.apache.lucene.index.CorruptIndexException

GeneMapping

public GeneMapping(GeneMappingConfiguration configuration)
            throws java.io.IOException,
                   GeneMappingException

Throws:

java.io.IOException

GeneMappingException

Method Detail

mapTopN

public java.util.ArrayList<SynHit> mapTopN(java.lang.String searchTerm,
                                           int topN)
                                    throws java.io.IOException,
                                           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:

GeneCandidateRetrievalException

java.io.IOException

map

public java.util.List<SynHit> map(java.lang.String searchTerm,
                                  org.apache.lucene.search.BooleanQuery contextQuery)
                           throws GeneMappingException

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:

java.lang.Exception

GeneMappingException

map

public MentionMappingResult map(GeneMention searchTerm,
                                org.apache.lucene.search.BooleanQuery contextQuery,
                                java.lang.String documentContext)
                         throws GeneMappingException

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:

java.lang.Exception

GeneMappingException

map

public DocumentMappingResult map(GeneDocument document)
                          throws GeneMappingException

Throws:

GeneMappingException

removeModifiers

public static java.lang.String removeModifiers(java.lang.String normalizedSearchTerm)

Parameters:

normalizedSearchTerm -

Returns:

the normalizedSearchTerm with all modifiers removed

removeUnspecifieds

public static java.lang.String removeUnspecifieds(java.lang.String normalizedSearchTerm)

removeNondescriptives

public static java.lang.String removeNondescriptives(java.lang.String normalizedSearchTerm)

removeDomainFamilies

public static java.lang.String removeDomainFamilies(java.lang.String normalizedSearchTerm)

removePremodifiers

public static java.lang.String removePremodifiers(java.lang.String normalizedSearchTerm)

getMappingCore

public MappingCore getMappingCore()

setMappingCore

public void setMappingCore(MappingCore mappingCore)

map

public MentionMappingResult map(java.lang.String term,
                                org.apache.lucene.search.BooleanQuery contextQuery,
                                java.lang.String documentContext)
                         throws GeneMappingException

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:

java.lang.Exception

GeneMappingException

getConfiguration

public GeneMappingConfiguration getConfiguration()