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Posted to commits@ctakes.apache.org by tm...@apache.org on 2014/10/14 23:50:10 UTC
svn commit: r1631897 -
/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/
Author: tmill
Date: Tue Oct 14 21:50:10 2014
New Revision: 1631897
URL: http://svn.apache.org/r1631897
Log:
CTAKES-280: Cleanup of assertion types for cleartk generic features.
Modified:
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AssertionAboveLeftTreeExtractor.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AssertionDependencyTreeExtractor.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/ContextWordWindowExtractor.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/TreeFragmentFeatureExtractor.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/UncertaintyFeatureExtractor.java
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AssertionAboveLeftTreeExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AssertionAboveLeftTreeExtractor.java?rev=1631897&r1=1631896&r2=1631897&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AssertionAboveLeftTreeExtractor.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AssertionAboveLeftTreeExtractor.java Tue Oct 14 21:50:10 2014
@@ -25,16 +25,16 @@ import java.util.List;
import org.apache.ctakes.assertion.util.SemanticClasses;
import org.apache.ctakes.core.resource.FileLocator;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.utils.tree.SimpleTree;
import org.apache.uima.jcas.JCas;
-import org.apache.uima.jcas.tcas.Annotation;
import org.cleartk.ml.Feature;
import org.cleartk.ml.TreeFeature;
import org.cleartk.ml.feature.extractor.CleartkExtractorException;
import org.cleartk.ml.feature.extractor.FeatureExtractor1;
import org.cleartk.util.CleartkInitializationException;
-public class AssertionAboveLeftTreeExtractor implements FeatureExtractor1 {
+public class AssertionAboveLeftTreeExtractor implements FeatureExtractor1<IdentifiedAnnotation> {
protected SemanticClasses sems = null;
public AssertionAboveLeftTreeExtractor() throws CleartkInitializationException{
@@ -46,9 +46,9 @@ public class AssertionAboveLeftTreeExtra
}
@Override
- public List<Feature> extract(JCas jcas, Annotation annotation)
+ public List<Feature> extract(JCas jcas, IdentifiedAnnotation annotation)
throws CleartkExtractorException {
- List<Feature> features = new ArrayList<Feature>();
+ List<Feature> features = new ArrayList<>();
SimpleTree tree = extractAboveLeftConceptTree(jcas, annotation, sems);
features.add(new TreeFeature("TK_AboveLeftTree", tree.toString()));
return features;
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AssertionDependencyTreeExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AssertionDependencyTreeExtractor.java?rev=1631897&r1=1631896&r2=1631897&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AssertionDependencyTreeExtractor.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AssertionDependencyTreeExtractor.java Tue Oct 14 21:50:10 2014
@@ -26,11 +26,11 @@ import org.apache.ctakes.assertion.util.
import org.apache.ctakes.assertion.util.SemanticClasses;
import org.apache.ctakes.core.resource.FileLocator;
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.ctakes.utils.tree.SimpleTree;
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.TreeFeature;
import org.cleartk.ml.feature.extractor.CleartkExtractorException;
@@ -39,7 +39,7 @@ import org.cleartk.util.CleartkInitializ
import com.google.common.collect.Lists;
-public class AssertionDependencyTreeExtractor implements FeatureExtractor1 {
+public class AssertionDependencyTreeExtractor implements FeatureExtractor1<IdentifiedAnnotation> {
protected SemanticClasses sems = null;
public AssertionDependencyTreeExtractor() throws CleartkInitializationException {
@@ -51,7 +51,7 @@ public class AssertionDependencyTreeExtr
}
@Override
- public List<Feature> extract(JCas jCas, Annotation arg1)
+ public List<Feature> extract(JCas jCas, IdentifiedAnnotation arg1)
throws CleartkExtractorException {
List<Feature> feats = Lists.newArrayList();
TreeFeature f1 = null;
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/ContextWordWindowExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/ContextWordWindowExtractor.java?rev=1631897&r1=1631896&r2=1631897&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/ContextWordWindowExtractor.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/ContextWordWindowExtractor.java Tue Oct 14 21:50:10 2014
@@ -28,15 +28,15 @@ import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+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 ContextWordWindowExtractor implements FeatureExtractor1 {
+public class ContextWordWindowExtractor implements FeatureExtractor1<IdentifiedAnnotation> {
private HashMap<String,Double> termVals = null;
private static final Pattern linePatt = Pattern.compile("^([^ ]+) : (.+)$");
@@ -82,7 +82,7 @@ public class ContextWordWindowExtractor
}
@Override
- public List<Feature> extract(JCas view, Annotation mention)
+ public List<Feature> extract(JCas view, IdentifiedAnnotation mention)
throws CleartkExtractorException {
ArrayList<Feature> feats = new ArrayList<Feature>();
List<Sentence> sents = JCasUtil.selectCovering(view, Sentence.class, mention.getBegin(), mention.getEnd());
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/TreeFragmentFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/TreeFragmentFeatureExtractor.java?rev=1631897&r1=1631896&r2=1631897&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/TreeFragmentFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/TreeFragmentFeatureExtractor.java Tue Oct 14 21:50:10 2014
@@ -26,10 +26,10 @@ import java.util.Scanner;
import org.apache.ctakes.assertion.util.SemanticClasses;
import org.apache.ctakes.core.resource.FileLocator;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.utils.tree.FragmentUtils;
import org.apache.ctakes.utils.tree.SimpleTree;
import org.apache.uima.jcas.JCas;
-import org.apache.uima.jcas.tcas.Annotation;
import org.cleartk.ml.Feature;
import org.cleartk.ml.feature.extractor.FeatureExtractor1;
import org.cleartk.util.CleartkInitializationException;
@@ -40,7 +40,7 @@ import org.cleartk.util.CleartkInitializ
* Model location is hardcoded as of right now.
* TODO: Parameterize this so that, e.g., multiple projects could use this feature if necessary.
*/
-public abstract class TreeFragmentFeatureExtractor implements FeatureExtractor1 {
+public abstract class TreeFragmentFeatureExtractor implements FeatureExtractor1<IdentifiedAnnotation> {
public static final String PARAM_OUTPUTDIR = "outputDir";
public static final String PARAM_SEMDIR = "semDir";
protected HashSet<SimpleTree> frags = null;
@@ -55,7 +55,6 @@ public abstract class TreeFragmentFeatur
}catch(Exception e){
throw new CleartkInitializationException(e, "org/apache/ctakes/assertion/all_cues.txt", "Could not find semantic classes resource.", new Object[]{});
}
-
}
private void initializeFrags(String resourceFilename){
@@ -74,5 +73,5 @@ public abstract class TreeFragmentFeatur
}
@Override
- public abstract List<Feature> extract(JCas jcas, Annotation annotation);
+ public abstract List<Feature> extract(JCas jcas, IdentifiedAnnotation annotation);
}
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/UncertaintyFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/UncertaintyFeatureExtractor.java?rev=1631897&r1=1631896&r2=1631897&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/UncertaintyFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/UncertaintyFeatureExtractor.java Tue Oct 14 21:50:10 2014
@@ -29,14 +29,14 @@ import org.cleartk.ml.Feature;
import org.cleartk.ml.feature.extractor.CleartkExtractorException;
import org.cleartk.ml.feature.extractor.FeatureExtractor1;
-public class UncertaintyFeatureExtractor implements FeatureExtractor1 {
+public class UncertaintyFeatureExtractor implements FeatureExtractor1<IdentifiedAnnotation> {
@Override
- public List<Feature> extract(JCas view, Annotation focusAnnotation)
+ public List<Feature> extract(JCas view, IdentifiedAnnotation focusAnnotation)
throws CleartkExtractorException {
- List<Feature> featList = new ArrayList<Feature>();
+ List<Feature> featList = new ArrayList<>();
- IdentifiedAnnotation mention = (IdentifiedAnnotation) focusAnnotation;
+ IdentifiedAnnotation mention = focusAnnotation;
featList.add(new Feature("IsNegated", mention.getPolarity() == CONST.NE_POLARITY_NEGATION_PRESENT));
return featList;
}