Package de.julielab.genemapper.genemodel

Class GeneDocumentFactory

java.lang.Object

de.julielab.genemapper.genemodel.GeneDocumentFactory

public class GeneDocumentFactory
extends Object

Constructor Summary

Constructors

Constructor	Description
GeneDocumentFactory(de.julielab.geneexpbase.configuration.Configuration configuration, de.julielab.speciesassignment.GeneSpeciesAssigner speciesAssigner, de.julielab.geneexpbase.TermNormalizer normalizer)

Method Summary

Modifier and Type	Method	Description
de.julielab.geneexpbase.genemodel.GeneDocument	createGeneDocument(org.apache.uima.jcas.JCas jCas, Map<String,Matcher> entityMappingTypes, Function<de.julielab.jcore.types.EntityMention,org.apache.commons.lang3.tuple.Pair<String,org.apache.lucene.search.BooleanQuery>> contextFun, de.julielab.geneexpbase.configuration.Parameters parameters)	Creates a document by setting all required information from the jCas.

Methods inherited from class java.lang.Object

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

Constructor Detail

GeneDocumentFactory

@Inject
public GeneDocumentFactory(de.julielab.geneexpbase.configuration.Configuration configuration,
                           de.julielab.speciesassignment.GeneSpeciesAssigner speciesAssigner,
                           de.julielab.geneexpbase.TermNormalizer normalizer)
                    throws de.julielab.geneexpbase.GeneExpException

Throws:

de.julielab.geneexpbase.GeneExpException

Method Detail

createGeneDocument

public de.julielab.geneexpbase.genemodel.GeneDocument createGeneDocument(org.apache.uima.jcas.JCas jCas,
                                                                         Map<String,Matcher> entityMappingTypes,
                                                                         Function<de.julielab.jcore.types.EntityMention,org.apache.commons.lang3.tuple.Pair<String,org.apache.lucene.search.BooleanQuery>> contextFun,
                                                                         de.julielab.geneexpbase.configuration.Parameters parameters)
                                                                  throws org.apache.uima.analysis_engine.AnalysisEngineProcessException

Creates a document by setting all required information from the jCas.

Items added are:

• Title text
• Text body
• Sentences
• PoS tags
• Chunks
• Acronyms
• MeSH Headings (from which species headings will be recognized)
• Species text mentions
• The genes, according to the entityMappingTypes. This is a mapping from qualified UIMA types to matchers that need to match the EntityMentions' specificType feature in order for the EntityMention to be used as a gene mention.

Parameters:

jCas - The JCas to create the GeneDocument form.

entityMappingTypes - This is a mapping from qualified UIMA types to matchers that need to match the EntityMentions' specificType feature in order for the EntityMention to be used as a gene mention.

contextFun - A function that delivers the context information for each gene mention.

parameters -

Throws:

org.apache.uima.analysis_engine.AnalysisEngineProcessException