Package de.julielab.jules.ae.genemapping.mappingcores

Class WeepingTreeMappingCore

java.lang.Object

de.julielab.jules.ae.genemapping.mappingcores.WeepingTreeMappingCore

All Implemented Interfaces:

MappingCore

public class WeepingTreeMappingCore
extends java.lang.Object
implements MappingCore

A rather relaxed mapping that doesn't try hard to disambiguate and does not filter out gene families or domains. This is basically just a gene synonym expansion mapping with minor name disambiguation at best.

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String	TAX_IDS	Configuration parameter.

Constructor Summary

Constructors

Constructor	Description
WeepingTreeMappingCore(GeneMappingConfiguration configuration)

Method Summary

Modifier and Type	Method	Description
CandidateRetrieval	getCandidateRetrieval()
SemanticDisambiguation	getSemanticDisambiguation()
TermNormalizer	getTermNormalizer()
DocumentMappingResult	map(GeneDocument document)
MentionMappingResult	map(GeneMention geneMention)

Methods inherited from class java.lang.Object

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

Field Detail

TAX_IDS

public static final java.lang.String TAX_IDS

Configuration parameter. Lists NCBI taxonomy IDs separated by commas. If this is given, only gene candidates belonging to at least one of the given taxonomy IDs will be taken into account.

See Also:

Constant Field Values

Constructor Detail

WeepingTreeMappingCore

public WeepingTreeMappingCore(GeneMappingConfiguration configuration)
                       throws GeneMappingException

Throws:

GeneMappingException

Method Detail

map

public MentionMappingResult map(GeneMention geneMention)
                         throws GeneMappingException

Specified by:

map in interface MappingCore

Throws:

GeneMappingException

getSemanticDisambiguation

public SemanticDisambiguation getSemanticDisambiguation()

Specified by:

getSemanticDisambiguation in interface MappingCore

getCandidateRetrieval

public CandidateRetrieval getCandidateRetrieval()

Specified by:

getCandidateRetrieval in interface MappingCore

getTermNormalizer

public TermNormalizer getTermNormalizer()

Specified by:

getTermNormalizer in interface MappingCore

map

public DocumentMappingResult map(GeneDocument document)
                          throws GeneMappingException

Specified by:

map in interface MappingCore

Throws:

GeneMappingException