Examples of org.apache.uima.cas.text.AnnotationIndex

org.apache.uima.cas.text.AnnotationIndex
An annotation index provides additional iterator functionality that applies only to instances of uima.tcas.Annotation. You can obtain an AnnotationIndex by calling:
AnnotationIndex idx = (AnnotationIndex)cas.getAnnotationIndex();
(the typecast is necessary for historical reasons).

Note that the AnnotationIndex defines the following sort order between two annotations:
- Annotations are sorted in increasing order of their start offset. That is, for any annotations a and b, if a.start < b.start then a < b.
- Annotations whose start offsets are equal are next sorted by decreasing order of their end offsets. That is, if a.start = b.start and a.end > b.end, then a < b. This causes annotations with larger to be sorted before annotations with smaller spans, which produces an iteration order similar to a preorder tree traversal.
- Annotations whose start offsets are equal and whose end offsets are equal are sorted based on {@link org.apache.uima.resource.metadata.TypePriorities} (which is an element of the componentdescriptor). That is, if a.start = b.start, a.end = b.end, and the type of a is defined before the type of b in the type priorities, then a < b.
- If none of the above rules apply, then the ordering is arbitrary. This will occur if you have two annotations of the exact same type that also have the same span. It will also occur if you have not defined any type priority between two annotations that have the same span.
In the method descriptions below, the notation a < b, where a and b are annotations, should be taken to mean a comes before b in the index, according to the above rules.


  }


  @Override
  public void process(JCas aJCas) {
    AnnotationIndex sentenceIdx = aJCas
        .getAnnotationIndex(Sentence.typeIndexID);
    AnnotationIndex neIdx = aJCas
        .getAnnotationIndex(IdentifiedAnnotation.typeIndexID);
    negateAnnotations(aJCas, sentenceIdx, neIdx,
        new NamedEntityTargetAnnoFilter());
    if (targetTypeName != null) {
      try {

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      // logger.setupDocument (getJCas ());


      FSIndex dbIndex = tcas.getAnnotationIndex(spanFeatureStructureType);
      FSIterator spanIterator = dbIndex.iterator();


      AnnotationIndex tokenIndex = (AnnotationIndex) tcas.getAnnotationIndex(tokenType);


      while (spanIterator.hasNext()) {
        ArrayList<AnnotationFS> tokens = new ArrayList<AnnotationFS>(2048);


        Annotation spanAnnotation = (Annotation) spanIterator.next();


        FSIterator tokenIter = tokenIndex.subiterator(spanAnnotation);


        // System.err.println ("Tokens:");


        // get all tokens for the specified block
        while (tokenIter.hasNext()) {

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  public void process(JCas aJCas) throws AnalysisEngineProcessException {


    ArrayList<TokenAnnotation> tokenList = new ArrayList<TokenAnnotation>();
    ArrayList<String> wordList = new ArrayList<String>();


    AnnotationIndex sentenceIndex = aJCas.getAnnotationIndex(SentenceAnnotation.type);
    AnnotationIndex tokenIndex = aJCas.getAnnotationIndex(TokenAnnotation.type);


    // iterate over Sentences
    FSIterator sentenceIterator = sentenceIndex.iterator();


    while (sentenceIterator.hasNext()) {
      SentenceAnnotation sentence = (SentenceAnnotation) sentenceIterator.next();


      tokenList.clear();
      wordList.clear();


      FSIterator tokenIterator = tokenIndex.subiterator(sentence);
      while (tokenIterator.hasNext()) {
        TokenAnnotation token = (TokenAnnotation) tokenIterator.next();


        tokenList.add(token);
        wordList.add(token.getCoveredText());

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    logger.info("process(JCas)");


    List<BaseToken> tokens = new ArrayList<BaseToken>();
    List<String> words = new ArrayList<String>();


    AnnotationIndex baseTokenIndex = jCas
        .getAnnotationIndex(BaseToken.type);


    FSIterator sentences = jCas.getAnnotationIndex(Sentence.type)
        .iterator();


    while (sentences.hasNext()) {
      Sentence sentence = (Sentence) sentences.next();


      tokens.clear();
      words.clear();


      FSIterator tokenIterator = baseTokenIndex.subiterator(sentence);
      while (tokenIterator.hasNext()) {
        BaseToken token = (BaseToken) tokenIterator.next();
        tokens.add(token);
        words.add(token.getCoveredText());
      }

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        iv_logger.info("process(JCas)");


      JFSIndexRepository indexes = jcas.getJFSIndexRepository();
      Iterator<?> sentItr = indexes.getAnnotationIndex(Sentence.type).iterator();
      AnnotationIndex baseTokenIndex = jcas.getJFSIndexRepository().getAnnotationIndex(
          org.apache.ctakes.typesystem.type.syntax.BaseToken.type);
      
      while (sentItr.hasNext()) {
        Sentence sentAnnot = (Sentence) sentItr.next();
        FSIterator btaItr = baseTokenIndex.subiterator(sentAnnot);


        // adapt JCas objects into objects expected by the Finite state
        // machines
        List<BaseToken> baseTokenList = new ArrayList<BaseToken>();
        while (btaItr.hasNext()) {

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//            out = new FileOutputStream(outputFile);
//            XCASSerializer.serialize(view.getCas(), out, true); // true -> formats the output
            outputFile.createNewFile();
            BufferedWriter bw = new BufferedWriter(new FileWriter(outputFile));


            AnnotationIndex nodeIndex = jCas.getAnnotationIndex(ConllDependencyNode.type);
            FSIterator sentences = jCas.getAnnotationIndex(Sentence.type).iterator();


            while (sentences.hasNext()) {
                Sentence sentence = (Sentence) sentences.next();




                ConllDependencyNode node = null;
                FSIterator nodeIterator = nodeIndex.subiterator(sentence);
                while (nodeIterator.hasNext()) {
//                    int pID = (node==null)? 0 : node.getID();
                    node = (ConllDependencyNode) nodeIterator.next();
                    
                    if (node.getId()!=0 ) { // && node.getID() !=pID) {

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  /** Returns the first ConllDependencyNode in the CAS w/ same begin and end as the given Annotation **/  
  public static ConllDependencyNode getDependencyNode(JCas jCas, Annotation annot) {


    AnnotationIndex nodeIndex = jCas.getAnnotationIndex(ConllDependencyNode.type);
      FSIterator nodeIterator = nodeIndex.iterator();
      while (nodeIterator.hasNext()) {
          ConllDependencyNode node = (ConllDependencyNode) nodeIterator.next();
          if (equalCoverage(annot,node)) {
            return node;
          }

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  }
  
  /** Returns the ConllDependencyNodes in the CAS w/ subsumed begins and ends **/  
  public static List<ConllDependencyNode> getDependencyNodes(JCas jCas, Annotation annot) {
    ArrayList<ConllDependencyNode> output = new ArrayList<ConllDependencyNode>();
    AnnotationIndex nodeIndex = jCas.getAnnotationIndex(ConllDependencyNode.type);
      FSIterator nodeIterator = nodeIndex.iterator();
      while (nodeIterator.hasNext()) {
          ConllDependencyNode node = (ConllDependencyNode) nodeIterator.next();
          if (doesSubsume(annot,node)) {
            output.add(node);
          }

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    logger.info(" process(JCas)");


    List<BaseToken> tokens = new ArrayList<BaseToken>();


    AnnotationIndex baseTokenIndex = jCas.getAnnotationIndex(BaseToken.type);
    FSIterator sentences = jCas.getAnnotationIndex(Sentence.type).iterator();


    while (sentences.hasNext()) {
      Sentence sentence = (Sentence) sentences.next();


      tokens.clear();


      FSIterator tokenIterator = baseTokenIndex.subiterator(sentence);
      while (tokenIterator.hasNext()) {
        BaseToken token = (BaseToken) tokenIterator.next();
        tokens.add(token);
      }

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    return tags;
  }


  private List<String> getCurrentTagList(JCas cas) {
    List<String> tagList = new ArrayList<String>();
    AnnotationIndex tokenIndex = cas.getAnnotationIndex(TokenAnnotation.type);
    FSIterator tokIt = tokenIndex.iterator();
    TokenAnnotation token = null;
    for (tokIt.moveToFirst(); tokIt.isValid(); tokIt.moveToNext()) {
      token = (TokenAnnotation) tokIt.get();
      tagList.add(token.getPosTag());
    }

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