Examples of org.apache.uima.cas.FSIterator

org.apache.uima.cas.FSIterator
Iterator over feature structures.
This iterator interface extends {@link java.util.Iterator}, and supports the standard hasNext and next methods. If finer control, including reverse iteration, is needed, see below.
Note: do not use the APIs described below *together* with the standard Java iterator methods next() and hasNext(). On any given iterator, use either the one or the other, but not both together. Otherwise, next/hasNext may exhibit incorrect behavior.
The FSIterator interface introduces the methods {@link #get()}, {@link #moveToNext()}, {@link #moveToPrevious()} methods. With these methods, retrieving thecurrent element (get) is a separate operation from moving the iterator (moveToNext and moveToPrevious. This makes the user's code less compact, but allows for finer control.
Specifically the get method is defined to return the same element that a call to next() would return, but does not advance the iterator.
Implementations of this interface are not required to be fail-fast. That is, if the iterator's collection is modified, the effects on the iterator are in general undefined. Some collections may handle this more gracefully than others, but in general, concurrent modification of the collection you're iterating over is a bad idea.
If the iterator is moved past the boundaries of the collection, the behavior of subsequent calls to {@link FSIterator#moveToNext() moveToNext()} or{@link FSIterator#moveToPrevious() moveToPrevious()} is undefined. For example, if a previouslyvalid iterator is invalidated by a call to {@link FSIterator#moveToNext() moveToNext()}, a subsequent call to {@link FSIterator#moveToPrevious() moveToPrevious()} is not guaranteed to setthe iterator back to the last element in the collection. Always use {@link FSIterator#moveToLast() moveToLast()} in such cases.

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


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


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


            FSIterator tokenIterator = tokenIndex.subiterator(sentence);
            while (tokenIterator.hasNext()) {
                tokens.add((BaseToken) tokenIterator.next());
            }
            //logger.info(" new sentence: ");
            FSIterator nodeIterator = nodeIndex.subiterator(sentence);
            while (nodeIterator.hasNext()) {
                ConllDependencyNode node = (ConllDependencyNode) nodeIterator.next();
                if (node.getId()!=0) {
                    nodes.add(node);
                }
                //logger.info(node.getFORM()+" ");
            }

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    this.jcas = jcas;


    // index the base tokens and NEs by their offsets
    hbs = new Hashtable<Integer, BaseToken>();
    hbe = new Hashtable<Integer, BaseToken>();
    FSIterator iter = jcas.getJFSIndexRepository().getAnnotationIndex(BaseToken.type).iterator();
    while (iter.hasNext()) {
      BaseToken t = (BaseToken) iter.next();
      hbs.put(t.getBegin(), t);
      hbe.put(t.getEnd(), t);
    }
  }

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      annot1.getCoveredText().contains(annot2.getCoveredText());
  }
  
  /** Find the sentence in which an Annotation lives **/
  public static Sentence getSentence( JCas jCas, Annotation annot ) {
    FSIterator sentences = jCas.getAnnotationIndex(Sentence.type).iterator();
    while (sentences.hasNext()) {
      Sentence sentence = (Sentence) sentences.next();
      if (doesSubsume(sentence,annot)) {
        return sentence;
      }
    }
    return null;

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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;
          }
      }
      return null;

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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);
          }
      }
      return output;

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


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


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


            tokens.clear();
            nodes.clear();


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


            FSIterator nodeIterator = nodeIndex.subiterator(sentence);
            while (nodeIterator.hasNext()) {
                ConllDependencyNode node = (ConllDependencyNode) nodeIterator.next();
                if (node.getId()!=0) {
                    nodes.add(node);
                }
            }

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    if (docId==null) docId = "141471681_1";
    System.out.print("creating vectors for "+docId);
//    Vector<Span> goldSpans = loadGoldStandard(docId, goldSpan2id);
    int numPos = 0;


    FSIterator markIter = jcas.getAnnotationIndex(Markable.type).iterator();
    LinkedList<Annotation> lm = FSIteratorToList.convert(markIter);


//    while(markIter.hasNext()){
//      Markable m = (Markable) markIter.next();
//      String key = m.getBegin() + "-" + m.getEnd();
//      markables.put(key, m);
//    }
    
    labeler = new GoldStandardLabeler(goldStandardDir, docId, lm);


//    Vector<Span> sysSpans = loadSystemPairs(lm, docId);
    // align the spans




    FSIterator iter = null;
//    FSIterator iter = jcas.getJFSIndexRepository().getAllIndexedFS(AnaphoricityVecInstance.type);
//    int numVecs = corefNodes.size();
//    log.info(numVecs + " nodes at the start of processing...");


//    if(anaphora){
//      while(iter.hasNext()){
//        AnaphoricityVecInstance vec = (AnaphoricityVecInstance) iter.next();
//        String nodeStr = vec.getVector();
//        int label = getLabel(nodeStr);
//        if(label == 1) posAnaphInst++;
//        else if(label == 0) negAnaphInst++;
//        anaphLabels.add(label);
//        svm_node[] nodes = SvmUtils.getNodes(nodeStr);
//        anaphNodes.add(nodes);
//      }
//      return;
//    }
    
    if(printVectors){
      try {
        neOut = new PrintWriter(outputDir + "/" + CorefConsts.NE + "/vectors/" + docId + ".libsvm");
        demOut = new PrintWriter(outputDir + "/" + CorefConsts.DEM + "/vectors/" + docId + ".libsvm");
        pronOut = new PrintWriter(outputDir + "/" + CorefConsts.PRON + "/vectors/"+ docId + ".libsvm");
      } catch (FileNotFoundException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
      }
    }


    //    int ind = 0;
    iter = jcas.getJFSIndexRepository().getAllIndexedFS(MarkablePairSet.type);
    while(iter.hasNext()){
      //      VecInstance vec = (VecInstance) iter.next();
      MarkablePairSet pair = (MarkablePairSet) iter.next();
      Markable anaphor = pair.getAnaphor();
      String corefType = (anaphor instanceof NEMarkable ? CorefConsts.NE : (anaphor instanceof DemMarkable ? CorefConsts.DEM : CorefConsts.PRON));
      //      String nodeStr = vec.getVector();
      //      int label = getLabel(nodeStr);
      FSList pairList = pair.getAntecedentList();

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  }


  // FIXME use parser output instead of LWA
  public String calcmNPHead () {
    Annotation a = m.getContent();
    FSIterator iter = jcas.getJFSIndexRepository().getAnnotationIndex(LookupWindowAnnotation.type).iterator();
    while (iter.hasNext()) {
      LookupWindowAnnotation lwa = (LookupWindowAnnotation) iter.next();
      if (lwa.getBegin()<=a.getBegin() && lwa.getEnd()==a.getEnd())
        return "yes";
    }
    return "no";
  }

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// the inclusionCondition resource (use parameter?) MarkableCreator
public class AnnotationSelector {


  public static ArrayList<Annotation> selectNE (JCas jcas) {
    ArrayList<Annotation> ret = new ArrayList<Annotation>();
    FSIterator iter = jcas.getJFSIndexRepository().getAnnotationIndex(EntityMention.type).iterator();
    while (iter.hasNext()) {
      EntityMention a = (EntityMention) iter.next();
      if(a.getOntologyConceptArr() != null)
//      int tid = a.getTypeID();
//      if (tid == TypeSystemConst.NE_TYPE_ID_ANATOMICAL_SITE ||
//        tid == TypeSystemConst.NE_TYPE_ID_DISORDER ||
//        tid == TypeSystemConst.NE_TYPE_ID_PROCEDURE ||

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    return ret;
  }


  public static ArrayList<BaseToken> selectBaseToken (JCas jcas) {
    ArrayList<BaseToken> ret = new ArrayList<BaseToken>();
    FSIterator iter = jcas.getJFSIndexRepository().getAnnotationIndex(BaseToken.type).iterator();
    while (iter.hasNext())
      ret.add((BaseToken)iter.next());
    java.util.Collections.sort(ret, new AnnotOffsetComparator());
    return ret;
  }

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