Examples of org.apache.uima.util.CasCopier

org.apache.uima.util.CasCopier
Utility class for doing deep copies of FeatureStructures from one CAS to another. To handle cases where the source CAS has multiple references to the same FS, you can create one instance of CasCopier and use it to copy multiple FeatureStructures. The CasCopier will remember previously copied FeatureStructures, so if you later copy another FS that has a reference to a previously copied FS, it will not duplicate the multiply-referenced FS.


      // copy gold EntityMentions and Modifiers to the system view
      List<IdentifiedAnnotation> goldMentions = new ArrayList<IdentifiedAnnotation>();
      goldMentions.addAll(JCasUtil.select(goldView, EntityMention.class));
      goldMentions.addAll(JCasUtil.select(goldView, Modifier.class));
      CasCopier copier = new CasCopier(goldView.getCas(), systemView.getCas());
      for (IdentifiedAnnotation goldMention : goldMentions)
      {
        Annotation copy = (Annotation) copier.copyFs(goldMention);
        Feature sofaFeature = copy.getType().getFeatureByBaseName("sofa");
        copy.setFeatureValue(sofaFeature, systemView.getSofa());
        copy.addToIndexes();
      }
    }

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    String docText = aJCas.getDocumentText();
    int prevDocLen = mDocBuf.length();
    mDocBuf.append(docText);


    // copy specified annotation types
    CasCopier copier = new CasCopier(aJCas.getCas(), mMergedCas.getCas());
    Set copiedIndexedFs = new HashSet(); // needed in case one annotation is in two indexes (could
    // happen if specified annotation types overlap)
    for (int i = 0; i < mAnnotationTypesToCopy.length; i++) {
      Type type = mMergedCas.getTypeSystem().getType(mAnnotationTypesToCopy[i]);
      FSIndex index = aJCas.getCas().getAnnotationIndex(type);
      Iterator iter = index.iterator();
      while (iter.hasNext()) {
        FeatureStructure fs = (FeatureStructure) iter.next();
        if (!copiedIndexedFs.contains(fs)) {
          Annotation copyOfFs = (Annotation) copier.copyFs(fs);
          // update begin and end
          copyOfFs.setBegin(copyOfFs.getBegin() + prevDocLen);
          copyOfFs.setEnd(copyOfFs.getEnd() + prevDocLen);
          mMergedCas.addFsToIndexes(copyOfFs);
          copiedIndexedFs.add(fs);

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      // copy gold EntityMentions and Modifiers to the system view
      List<IdentifiedAnnotation> goldMentions = new ArrayList<IdentifiedAnnotation>();
      goldMentions.addAll(JCasUtil.select(goldView, EntityMention.class));
      goldMentions.addAll(JCasUtil.select(goldView, Modifier.class));
      CasCopier copier = new CasCopier(goldView.getCas(), systemView.getCas());
      for (IdentifiedAnnotation goldMention : goldMentions)
      {
        Annotation copy = (Annotation) copier.copyFs(goldMention);
        Feature sofaFeature = copy.getType().getFeatureByBaseName("sofa");
        copy.setFeatureValue(sofaFeature, systemView.getSofa());
        copy.addToIndexes();
      }
    }

View Full Code Here

      // copy gold Mentions and Modifiers to the system view
      List<IdentifiedAnnotation> goldMentions = new ArrayList<IdentifiedAnnotation>();
      goldMentions.addAll(JCasUtil.select(goldView, EventMention.class));
      goldMentions.addAll(JCasUtil.select(goldView, EntityMention.class));
      goldMentions.addAll(JCasUtil.select(goldView, Modifier.class));
      CasCopier copier = new CasCopier(goldView.getCas(), systemView.getCas());
      Feature sofaFeature = jCas.getTypeSystem().getFeatureByFullName(CAS.FEATURE_FULL_NAME_SOFA);
      for (IdentifiedAnnotation goldMention : goldMentions) {
        Annotation copy = (Annotation) copier.copyFs(goldMention);
        copy.setFeatureValue(sofaFeature, systemView.getSofa());
        copy.addToIndexes();
      }


      // copy gold relations to the system view
      for (BinaryTextRelation goldRelation : JCasUtil.select(goldView, BinaryTextRelation.class)) {
        BinaryTextRelation relation = (BinaryTextRelation) copier.copyFs(goldRelation);
        relation.addToIndexes(systemView);
        for (RelationArgument relArg : Lists.newArrayList(relation.getArg1(), relation.getArg2())) {
          relArg.addToIndexes(systemView);
          // relArg.getArgument() should have been added to indexes with
          // mentions above

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      // copy gold Mentions and Modifiers to the system view
      List<IdentifiedAnnotation> goldMentions = new ArrayList<IdentifiedAnnotation>();
      goldMentions.addAll(JCasUtil.select(goldView, EventMention.class));
      goldMentions.addAll(JCasUtil.select(goldView, EntityMention.class));
      goldMentions.addAll(JCasUtil.select(goldView, Modifier.class));
      CasCopier copier = new CasCopier(goldView.getCas(), systemView.getCas());
      for (IdentifiedAnnotation goldMention : goldMentions) {
        Annotation copy = (Annotation) copier.copyFs(goldMention);
        Feature sofaFeature = copy.getType().getFeatureByBaseName("sofa");
        copy.setFeatureValue(sofaFeature, systemView.getSofa());
        copy.addToIndexes();
      }
    }

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    JCas modview = fromJcas.getView(toView);


    Set<Annotation> indexedFs = new HashSet<Annotation>();
    AnnotationIndex<Annotation> annotationIndex = fromJcas.getAnnotationIndex();


    CasCopier casCopier = new CasCopier(fromJcas.getCas(), modview.getCas());
    for (Annotation annotation : annotationIndex) {
      // TODO be careful here, because some people inherit from DocumentAnnotation
      if (annotation instanceof DocumentAnnotation) {
        continue;
      }
      Annotation clone = (Annotation) casCopier.copyFs(annotation);
      // change the view/sofa of the new annotation...
      // see: http://osdir.com/ml/apache.uima.general/2007-09/msg00107.html
      clone.setFeatureValue(modview.getTypeSystem()
              .getFeatureByFullName(CAS.FEATURE_FULL_NAME_SOFA), modview.getSofa());
      final int mappedBegin = map[clone.getBegin()];

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    Set<Annotation> indexedFs = new HashSet<Annotation>();
    AnnotationIndex<Annotation> annotationIndex = fromJcas.getAnnotationIndex();
    TypeSystem typeSystem = fromJcas.getTypeSystem();
    Type docType = typeSystem.getType(UIMAConstants.TYPE_DOCUMENT);
    CasCopier casCopier = new CasCopier(fromJcas.getCas(), modview.getCas());
    for (Annotation annotation : annotationIndex) {
      // TODO be careful here, because some people inherit from DocumentAnnotation
      if (typeSystem.subsumes(docType, annotation.getType())) {
        continue;
      }
      Annotation clone = (Annotation) casCopier.copyFs(annotation);
      // change the view/sofa of the new annotation...
      // see: http://osdir.com/ml/apache.uima.general/2007-09/msg00107.html
      clone.setFeatureValue(modview.getTypeSystem()
              .getFeatureByFullName(CAS.FEATURE_FULL_NAME_SOFA), modview.getSofa());
      final int mappedBegin = map[clone.getBegin()];

View Full Code Here


      // copy gold EntityMentions and Modifiers to the system view
      List<IdentifiedAnnotation> goldMentions = new ArrayList<IdentifiedAnnotation>();
      goldMentions.addAll(JCasUtil.select(goldView, EntityMention.class));
      goldMentions.addAll(JCasUtil.select(goldView, Modifier.class));
      CasCopier copier = new CasCopier(goldView.getCas(), systemView.getCas());
      for (IdentifiedAnnotation goldMention : goldMentions)
      {
        Annotation copy = (Annotation) copier.copyFs(goldMention);
        Feature sofaFeature = copy.getType().getFeatureByBaseName("sofa");
        copy.setFeatureValue(sofaFeature, systemView.getSofa());
        copy.addToIndexes();
      }
    }

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      // copy cTAKES EntityMentions and Modifiers to gold view
      List<IdentifiedAnnotation> cTakesMentions = new ArrayList<IdentifiedAnnotation>();
      cTakesMentions.addAll(JCasUtil.select(systemView, EntityMention.class));
      cTakesMentions.addAll(JCasUtil.select(systemView, Modifier.class));
      CasCopier copier = new CasCopier(systemView.getCas(), goldView.getCas());
      for (IdentifiedAnnotation cTakesMention : cTakesMentions)
      {
        Annotation copy = (Annotation) copier.copyFs(cTakesMention);
        Feature sofaFeature = copy.getType().getFeatureByBaseName("sofa");
        copy.setFeatureValue(sofaFeature, goldView.getSofa());
        copy.addToIndexes();
      }

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