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Posted to commits@ctakes.apache.org by tm...@apache.org on 2014/10/15 18:02:45 UTC
svn commit: r1632103 - in
/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk:
./ extractors/
Author: tmill
Date: Wed Oct 15 16:02:45 2014
New Revision: 1632103
URL: http://svn.apache.org/r1632103
Log:
Corrected a bunch of type issues in assertion inherited from parent class.
Modified:
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityCleartkAnalysisEngine.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityFedaCleartkAnalysisEngine.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/ExtractorListFeatureFunctionConverter.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/NegationDependencyFeatureExtractor.java
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java?rev=1632103&r1=1632102&r2=1632103&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java Wed Oct 15 16:02:45 2014
@@ -65,7 +65,7 @@ public class GenericCleartkAnalysisEngin
// new CleartkExtractor(
// IdentifiedAnnotation.class, new GenericFeaturesExtractor()) );
if(this.entityFeatureExtractors == null){
- this.entityFeatureExtractors = new ArrayList<FeatureExtractor1>();
+ this.entityFeatureExtractors = new ArrayList<>();
}
this.entityFeatureExtractors.add(new ContextWordWindowExtractor("org/apache/ctakes/assertion/models/generic.txt"));
this.entityFeatureExtractors.add(new GenericFeaturesExtractor());
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java?rev=1632103&r1=1632102&r2=1632103&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java Wed Oct 15 16:02:45 2014
@@ -67,7 +67,7 @@ public class HistoryCleartkAnalysisEngin
// IdentifiedAnnotation.class, new HistoryFeaturesExtractor()) );
//
if(this.entityFeatureExtractors == null){
- this.entityFeatureExtractors = new ArrayList<FeatureExtractor1>();
+ this.entityFeatureExtractors = new ArrayList<>();
}
this.entityFeatureExtractors.add(new ContextWordWindowExtractor("org/apache/ctakes/assertion/models/history.txt"));
this.entityFeatureExtractors.add(new HistoryFeaturesExtractor());
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityCleartkAnalysisEngine.java?rev=1632103&r1=1632102&r2=1632103&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityCleartkAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityCleartkAnalysisEngine.java Wed Oct 15 16:02:45 2014
@@ -54,7 +54,7 @@ public class PolarityCleartkAnalysisEngi
probabilityOfKeepingADefaultExample = 1.0; //0.1;
if(this.entityFeatureExtractors == null){
- this.entityFeatureExtractors = new ArrayList<FeatureExtractor1>();
+ this.entityFeatureExtractors = new ArrayList<>();
}
// polarity keyword list:
@@ -64,7 +64,8 @@ public class PolarityCleartkAnalysisEngi
// stk frags feature:
if(featConfig == FEATURE_CONFIG.STK_FRAGS || featConfig == FEATURE_CONFIG.ALL_SYN){
- this.entityFeatureExtractors.add(new AboveLeftFragmentExtractor("AL_Polarity","org/apache/ctakes/assertion/models/jbi_paper_polarity_sems_frags.txt"));
+// this.entityFeatureExtractors.add(new AboveLeftFragmentExtractor("AL_Polarity","org/apache/ctakes/assertion/models/jbi_paper_polarity_sems_frags.txt"));
+ this.entityFeatureExtractors.add(new AboveLeftFragmentExtractor("AL_Polarity","org/apache/ctakes/assertion/models/sharpPolarityFrags.txt"));
// this.entityFeatureExtractors.add(new ConceptModifierPETFragmentExtractor("NegRel", "org/apache/ctakes/assertion/models/polarityRelnFragsStrat.txt"));
}
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityFedaCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityFedaCleartkAnalysisEngine.java?rev=1632103&r1=1632102&r2=1632103&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityFedaCleartkAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityFedaCleartkAnalysisEngine.java Wed Oct 15 16:02:45 2014
@@ -34,22 +34,18 @@ import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.resource.ResourceInitializationException;
import org.cleartk.ml.Instance;
-import org.cleartk.ml.feature.extractor.FeatureExtractor1;
import org.cleartk.ml.feature.function.FeatureFunctionExtractor;
public class PolarityFedaCleartkAnalysisEngine extends PolarityCleartkAnalysisEngine {
- public static final String NEGATED = "NEGATED";
- public static final String NOT_NEGATED = "NOT_NEGATED";
-
@Override
public void initialize(UimaContext context) throws ResourceInitializationException {
super.initialize(context);
probabilityOfKeepingADefaultExample = 1.0; //0.1;
if(this.entityFeatureExtractors == null){
- this.entityFeatureExtractors = new ArrayList<FeatureExtractor1>();
+ this.entityFeatureExtractors = new ArrayList<>();
}
this.entityFeatureExtractors.add(new NegationDependencyFeatureExtractor());
this.entityFeatureExtractors.add(new ContextWordWindowExtractor("org/apache/ctakes/assertion/models/polarity.txt"));
@@ -96,7 +92,7 @@ public class PolarityFedaCleartkAnalysis
}
}
public static FeatureSelection<String> createFeatureSelection(double threshold) {
- return new Chi2FeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME, threshold, false);
+ return new Chi2FeatureSelection<>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME, threshold, false);
// return new MutualInformationFeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME);
}
@@ -106,20 +102,20 @@ public class PolarityFedaCleartkAnalysis
private void initializeDomainAdaptation() {
// Do domain adaptation
- featureFunctionExtractors = new ArrayList<FeatureFunctionExtractor>();
+ featureFunctionExtractors = new ArrayList<>();
// FedaFeatureFunction ff = new FedaFeatureFunction(new ArrayList<String>(trainFileToDomain.values()));
featureFunctionExtractors.addAll(ExtractorListFeatureFunctionConverter.convert(contextFeatureExtractors, ffDomainAdaptor));
featureFunctionExtractors.addAll(ExtractorListFeatureFunctionConverter.convert(tokenContextFeatureExtractors, ffDomainAdaptor));
featureFunctionExtractors.addAll(ExtractorListFeatureFunctionConverter.convert(tokenCleartkExtractors, ffDomainAdaptor));
featureFunctionExtractors.addAll(ExtractorListFeatureFunctionConverter.convert(entityFeatureExtractors, ffDomainAdaptor));
- featureFunctionExtractors.add(new FeatureFunctionExtractor(cuePhraseInWindowExtractor, ffDomainAdaptor));
+ featureFunctionExtractors.add(new FeatureFunctionExtractor<>(cuePhraseInWindowExtractor, ffDomainAdaptor));
}
@Override
protected void initializeFeatureSelection() throws ResourceInitializationException {
if (featureSelectionThreshold == 0) {
this.featureSelection = null;
} else {
- this.featureSelection = this.createFeatureSelection(this.featureSelectionThreshold);
+ this.featureSelection = createFeatureSelection(this.featureSelectionThreshold);
// if ( (new File(this.featureSelectionURI)).exists() ) {
// try {
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/ExtractorListFeatureFunctionConverter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/ExtractorListFeatureFunctionConverter.java?rev=1632103&r1=1632102&r2=1632103&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/ExtractorListFeatureFunctionConverter.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/ExtractorListFeatureFunctionConverter.java Wed Oct 15 16:02:45 2014
@@ -21,18 +21,19 @@ package org.apache.ctakes.assertion.medf
import java.util.ArrayList;
import java.util.List;
+import org.apache.uima.jcas.tcas.Annotation;
import org.cleartk.ml.feature.extractor.FeatureExtractor1;
import org.cleartk.ml.feature.function.FeatureFunction;
import org.cleartk.ml.feature.function.FeatureFunctionExtractor;
public class ExtractorListFeatureFunctionConverter {
- public static List<FeatureFunctionExtractor> convert( List<? extends FeatureExtractor1> extractors, FeatureFunction ff ) {
+ public static <T extends Annotation> List<FeatureFunctionExtractor<T>> convert( List<? extends FeatureExtractor1<T>> extractors, FeatureFunction ff ) {
- List<FeatureFunctionExtractor> featureFunctionExtractors = new ArrayList<FeatureFunctionExtractor>();
+ List<FeatureFunctionExtractor<T>> featureFunctionExtractors = new ArrayList<>();
if (null!=extractors) {
- for (FeatureExtractor1 extractor : extractors) {
+ for (FeatureExtractor1<T> extractor : extractors) {
featureFunctionExtractors.add(
- new FeatureFunctionExtractor(extractor,ff)
+ new FeatureFunctionExtractor<>(extractor,ff)
);
}
}
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/NegationDependencyFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/NegationDependencyFeatureExtractor.java?rev=1632103&r1=1632102&r2=1632103&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/NegationDependencyFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/NegationDependencyFeatureExtractor.java Wed Oct 15 16:02:45 2014
@@ -24,16 +24,16 @@ import java.util.List;
import org.apache.ctakes.assertion.util.NegationManualDepContextAnalyzer;
import org.apache.ctakes.dependency.parser.util.DependencyUtility;
import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
-import org.apache.uima.jcas.tcas.Annotation;
import org.cleartk.ml.Feature;
import org.cleartk.ml.feature.extractor.CleartkExtractorException;
import org.cleartk.ml.feature.extractor.FeatureExtractor1;
public class NegationDependencyFeatureExtractor implements
- FeatureExtractor1 {
+ FeatureExtractor1<IdentifiedAnnotation> {
NegationManualDepContextAnalyzer conAnal = null;
@@ -42,9 +42,9 @@ public class NegationDependencyFeatureEx
}
@Override
- public List<Feature> extract(JCas jcas, Annotation focusAnnotation)
+ public List<Feature> extract(JCas jcas, IdentifiedAnnotation focusAnnotation)
throws CleartkExtractorException {
- List<Feature> feats = new ArrayList<Feature>();
+ List<Feature> feats = new ArrayList<>();
Sentence sent = null;
List<Sentence> sents = JCasUtil.selectCovering(jcas, Sentence.class, focusAnnotation.getBegin(), focusAnnotation.getEnd());