ch.epfl.bbp.uima.ae.relations

Class ExtractCoocurrences

java.lang.Object

org.apache.uima.analysis_component.AnalysisComponent_ImplBase

org.apache.uima.analysis_component.Annotator_ImplBase

org.apache.uima.analysis_component.JCasAnnotator_ImplBase

org.apache.uima.fit.component.JCasAnnotator_ImplBase

ch.epfl.bbp.uima.ae.relations.ExtractCoocurrences

All Implemented Interfaces:

org.apache.uima.analysis_component.AnalysisComponent

Direct Known Subclasses:

ExtractCoocurrencesFilterDistance, ExtractSameCoocurrences

public class ExtractCoocurrences
extends org.apache.uima.fit.component.JCasAnnotator_ImplBase

Extracts cooccurrences

Author:

renaud.richardet@epfl.ch

See Also:

WriteCoocurrencesToLoadfile to write these cooccurrences to a file

Field Summary

Fields

Modifier and Type	Field and Description
protected Class<? extends org.apache.uima.jcas.tcas.Annotation>	annotation1
protected Class<? extends org.apache.uima.jcas.tcas.Annotation>	annotation2
protected String	annotationStr1
protected String	annotationStr2
protected String	cooccurrenceType
protected Class<? extends org.apache.uima.jcas.tcas.Annotation>	enclosingScope
protected String	enclosingScopeStr
protected String[]	firstIdFields
protected String	firstIdFieldsRaw
protected List<Method>	firstIdMethods
protected boolean	keepOnlyNearestNeighbors
protected static org.slf4j.Logger	LOG
static String	PARAM_KEEP_ONLY_NEAREST_NEIGHBORS
protected String[]	secondIdFields
protected String	secondIdFieldsRaw
protected List<Method>	secondIdMethods

Constructor Summary

Constructors

Constructor and Description
ExtractCoocurrences()

Method Summary

Methods

Modifier and Type	Method and Description
protected Cooccurrence	filterCooccurence(org.apache.uima.jcas.JCas jCas, org.apache.uima.jcas.tcas.Annotation enclosingAnnot, org.apache.uima.jcas.tcas.Annotation annot1, org.apache.uima.jcas.tcas.Annotation annot2, String[] firstIds, String[] secondIds) Adds all cooccurrences (no filtering).
void	initialize(org.apache.uima.UimaContext context)
void	process(org.apache.uima.jcas.JCas jCas)

Methods inherited from class org.apache.uima.fit.component.JCasAnnotator_ImplBase

getLogger

Methods inherited from class org.apache.uima.analysis_component.JCasAnnotator_ImplBase

getRequiredCasInterface, process

Methods inherited from class org.apache.uima.analysis_component.Annotator_ImplBase

getCasInstancesRequired, hasNext, next

Methods inherited from class org.apache.uima.analysis_component.AnalysisComponent_ImplBase

batchProcessComplete, collectionProcessComplete, destroy, getContext, getResultSpecification, reconfigure, setResultSpecification

Methods inherited from class java.lang.Object

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

Field Detail

LOG

protected static org.slf4j.Logger LOG

enclosingScopeStr

protected String enclosingScopeStr

enclosingScope

protected Class<? extends org.apache.uima.jcas.tcas.Annotation> enclosingScope

annotationStr1

protected String annotationStr1

annotation1

protected Class<? extends org.apache.uima.jcas.tcas.Annotation> annotation1

firstIdFieldsRaw

protected String firstIdFieldsRaw

firstIdFields

protected String[] firstIdFields

firstIdMethods

protected List<Method> firstIdMethods

annotationStr2

protected String annotationStr2

annotation2

protected Class<? extends org.apache.uima.jcas.tcas.Annotation> annotation2

secondIdFieldsRaw

protected String secondIdFieldsRaw

secondIdFields

protected String[] secondIdFields

secondIdMethods

protected List<Method> secondIdMethods

cooccurrenceType

protected String cooccurrenceType

PARAM_KEEP_ONLY_NEAREST_NEIGHBORS

public static final String PARAM_KEEP_ONLY_NEAREST_NEIGHBORS

See Also:

Constant Field Values

keepOnlyNearestNeighbors

protected boolean keepOnlyNearestNeighbors

Constructor Detail

ExtractCoocurrences

public ExtractCoocurrences()

Method Detail

initialize

public void initialize(org.apache.uima.UimaContext context)
                throws org.apache.uima.resource.ResourceInitializationException

Specified by:

initialize in interface org.apache.uima.analysis_component.AnalysisComponent

Overrides:

initialize in class org.apache.uima.fit.component.JCasAnnotator_ImplBase

Throws:

org.apache.uima.resource.ResourceInitializationException

process

public void process(org.apache.uima.jcas.JCas jCas)
             throws org.apache.uima.analysis_engine.AnalysisEngineProcessException

Specified by:

process in class org.apache.uima.analysis_component.JCasAnnotator_ImplBase

Throws:

org.apache.uima.analysis_engine.AnalysisEngineProcessException

filterCooccurence

protected Cooccurrence filterCooccurence(org.apache.uima.jcas.JCas jCas,
                             org.apache.uima.jcas.tcas.Annotation enclosingAnnot,
                             org.apache.uima.jcas.tcas.Annotation annot1,
                             org.apache.uima.jcas.tcas.Annotation annot2,
                             String[] firstIds,
                             String[] secondIds)

Adds all cooccurrences (no filtering). Subclasses can implement finer filtering.

Parameters:

jCas -

enclosingAnnot -

annot1 -

annot2 -

firstIds -

firstIds -