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.

   * @param aCAS
   *          CAS from which annotations will be extracted
   */
  private TreeNode buildTree(CAS aCAS) throws CASException {
    // get iterator over all annotations
    FSIterator iterator = aCAS.getAnnotationIndex().iterator();


    // create artifical root node encompassing entire document
    DefaultMutableTreeNode root = new DefaultMutableTreeNode("Document");
    // add children to this node
    _buildTree(root, iterator, 0, aCAS.getDocumentText().length());

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    } catch (CASException e) {
      throw new ResourceProcessException(e);
    }


    // retreive the filename of the input file from the CAS
    FSIterator it = jcas.getAnnotationIndex(SourceDocumentInformation.type).iterator();
    File outFile = null;
    if (it.hasNext()) {
      SourceDocumentInformation fileLoc = (SourceDocumentInformation) it.next();
      File inFile;
      try {
        inFile = new File(new URL(fileLoc.getUri()).getPath());
        String outFileName = inFile.getName();
        if (fileLoc.getOffsetInSource() > 0) {

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  public void testAddAnnotationToTree() throws Exception {
    try {
      // create an annotation
      createExampleFS(this.cas);
      FSIterator iter = this.cas.getAnnotationIndex(exampleType).iterator();
      AnnotationFS annot = (AnnotationFS) iter.get();


      // init viewer
      viewer.setCAS(this.cas);


      // add to tree

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      entityCount++;
      int dataSize = 0;
      // get size here
      Type t = aCas.getTypeSystem().getType("uima.cpm.FileLocation");
      Feature f = t.getFeatureByBaseName("DocumentSize");
      FSIterator fsI = aCas.getAnnotationIndex(t).iterator();
      if (fsI.isValid()) {
        dataSize = fsI.get().getIntValue(f);
      }


      size += dataSize;
      // to handle exceptions occured in any of the components for the entity
      if (aStatus.isException()) {

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  public void process(JCas aJCas) throws AnalysisEngineProcessException {
    mDoc = aJCas.getDocumentText();
    mPos = 0;
    // retreive the filename of the input file from the CAS so that it can be added
    // to each segment
    FSIterator it = aJCas.getAnnotationIndex(SourceDocumentInformation.type).iterator();
    if (it.hasNext()) {
      SourceDocumentInformation fileLoc = (SourceDocumentInformation) it.next();
      mDocUri = fileLoc.getUri();
    } else {
      mDocUri = null;
    }
  }

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    } catch (CASException e) {
      throw new ResourceProcessException(e);
    }


    // retreive the filename of the input file from the CAS
    FSIterator it = jcas.getAnnotationIndex(SourceDocumentInformation.type).iterator();
    File outFile = null;
    if (it.hasNext()) {
      SourceDocumentInformation fileLoc = (SourceDocumentInformation) it.next();
      File inFile;
      try {
        inFile = new File(new URL(fileLoc.getUri()).getPath());
        outFile = new File(mOutputDir, inFile.getName());
      } catch (MalformedURLException e1) {

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    HashMap types = processTofs(aCAS, this.tofs);


    try
    {
      //iterate and print annotations
      FSIterator typeIterator = aCAS.getAnnotationIndex().iterator();


      for (typeIterator.moveToFirst(); typeIterator.isValid(); typeIterator.moveToNext())
      {
        Iterator it = types.keySet().iterator();


        while (it.hasNext())
        {
          //get current type and features
          Type currentType = (Type) it.next();
          boolean isFeatureOnly = false;
          
          ArrayList featureList = (ArrayList) types.get(currentType);
          if(featureList.size() >0 && featureList.get(0).equals(featureOnlyKey)){
            featureList.remove(0);
            isFeatureOnly = true;
          }
          Feature[] features = (Feature[]) featureList.toArray(new Feature[] {
          });
          
          AnnotationFS annot = (AnnotationFS) typeIterator.get();


          if (annot.getType().getName() == currentType.getName())
          {
            //only for formatting necessary
            boolean firstFeature = true;

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    // prettyPrint
    CAS englishView = cas.getView("EnglishDocument");
    assertNotNull(englishView);
    assertNotNull(englishView.getSofa());
    FSIndex index = englishView.getAnnotationIndex();
    FSIterator iter = index.iterator();
    // skip document annotation
    AnnotationFS fs = (AnnotationFS) iter.get();
    iter.moveToNext();


    // the exampleType fs
    fs = (AnnotationFS) iter.get();
    FeatureStructureImplC fsImpl = (FeatureStructureImplC) fs;
    StringBuffer sb = new StringBuffer(1024);
    fsImpl.prettyPrint(2, 1, sb, true);
    // System.out.println(sb.toString());
  }

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  public void testClone() throws Exception {
    createExampleFS(cas);
    // get the example FS
    CAS englishView = cas.getView("EnglishDocument");
    FSIterator iter = englishView.getAnnotationIndex().iterator();
    // skip document annotation
    iter.moveToNext();
    // the exampleType fs
    AnnotationFS fs = (AnnotationFS) iter.get();


    // clone it
    AnnotationFS clone = (AnnotationFS) fs.clone();


    // subsitute the clone for the original in the index,

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    // Add an FS with an array of existing annotations in another view
    int nToks = 3;
    ArrayFS array = newView2.createArrayFS(nToks);
    Type thingType = newCas2.getTypeSystem().getType("org.apache.uima.testTypeSystem.Thing");
    FSIterator thingIter = newCas2.getAnnotationIndex(thingType).iterator();
    for (int i = 0; i < nToks; ++i)
      array.set(i, (FeatureStructure)thingIter.next());  
    Type annotArrayTestType = newView2.getTypeSystem().getType("org.apache.uima.testTypeSystem.AnnotationArrayTest");
    Feature annotArrayFeat = annotArrayTestType.getFeatureByBaseName("arrayOfAnnotations");
    AnnotationFS fsArrayTestAnno = newView2.createAnnotation(annotArrayTestType, 13, 27);
    fsArrayTestAnno.setFeatureValue(annotArrayFeat,array);
    newView2.addFsToIndexes(fsArrayTestAnno);
    
    // re-serialize each new CAS back to XMI, keeping consistent ids
    String newSerCas1 = serialize(newCas1, deserSharedData1, marker1);
    String newSerCas2 = serialize(newCas2, deserSharedData2, marker2);
    
    // merge the two XMI CASes back into the original CAS
    // the shared data will be reset and recreated if not using deltaCas
    if (useDeltas) {
      deserialize(newSerCas1, cas, serSharedData, false, maxOutgoingXmiId);
    } else {
      deserialize(newSerCas1, cas, serSharedData, false, -1);
    }
    assertEquals(numAnnotations + 2, cas.getAnnotationIndex().size());


    deserialize(newSerCas2, cas, serSharedData, false, maxOutgoingXmiId);
    assertEquals(numAnnotations + 5, cas.getAnnotationIndex().size());
    assertEquals(docText, cas.getDocumentText());


    // Serialize/deserialize again in case merge created duplicate ids
    String newSerCasMerged = serialize(cas, serSharedData);
    deserialize(newSerCasMerged, cas, serSharedData, false, -1);
    
    //check covered text of annotations
    FSIterator iter = cas.getAnnotationIndex().iterator();
    while (iter.hasNext()) {
      AnnotationFS annot = (AnnotationFS)iter.next();
      assertEquals(cas.getDocumentText().substring(
              annot.getBegin(), annot.getEnd()), annot.getCoveredText());
    }
    //check Owner annotation we created to test link across merge boundary
    iter = cas.getAnnotationIndex(ownerType).iterator();
    while (iter.hasNext()) {
      AnnotationFS
      annot = (AnnotationFS)iter.next();
      String componentId = annot.getStringValue(componentIdFeat);
      if ("XCasDeserializerTest".equals(componentId)) {
        FeatureStructure targetRelArgs = annot.getFeatureValue(argsFeat);
        AnnotationFS targetDomain = (AnnotationFS)targetRelArgs.getFeatureValue(domainFeat);
        assertEquals(60, targetDomain.getBegin());
        assertEquals(70, targetDomain.getEnd());
        AnnotationFS targetRange = (AnnotationFS)targetRelArgs.getFeatureValue(rangeFeat);
        assertEquals(orgBegin, targetRange.getBegin());
        assertEquals(orgEnd, targetRange.getEnd());
      }     
    } 
    //check Sofas
    CAS targetView1 = cas.getView("newSofa1");
    assertEquals(sofaText1, targetView1.getDocumentText());
    CAS targetView2 = cas.getView("newSofa2");
    assertEquals(sofaText2, targetView2.getDocumentText());
    AnnotationFS targetAnnot1 = (AnnotationFS) 
      targetView1.getAnnotationIndex(orgType).iterator().get();
    assertEquals(annotText, targetAnnot1.getCoveredText());
    AnnotationFS targetAnnot2 = (AnnotationFS) 
    targetView2.getAnnotationIndex(orgType).iterator().get();
    assertEquals(annotText, targetAnnot2.getCoveredText());
    assertTrue(targetView1.getSofa().getSofaRef() != 
            targetView2.getSofa().getSofaRef());
    
    CAS checkPreexistingView = cas.getView("preexistingView");
    assertEquals(preexistingViewText, checkPreexistingView.getDocumentText());
    Type personType = cas.getTypeSystem().getType("org.apache.uima.testTypeSystem.Person");    
    AnnotationFS targetAnnot3 = (AnnotationFS)
            checkPreexistingView.getAnnotationIndex(personType).iterator().get();
    assertEquals("John Smith", targetAnnot3.getCoveredText());


    // Check the FS with an array of pre-existing FSs
    iter = targetView2.getAnnotationIndex(annotArrayTestType).iterator();
    componentIdFeat = thingType.getFeatureByBaseName("componentId");
    while (iter.hasNext()) {
      AnnotationFS annot = (AnnotationFS)iter.next();
      ArrayFS fsArray = (ArrayFS)annot.getFeatureValue(annotArrayFeat);
      assertTrue(fsArray.size() == 3);
      for (int i = 0; i < fsArray.size(); ++i) {
        AnnotationFS refAnno = (AnnotationFS)fsArray.get(i);
        assertEquals(thingType.getName(), refAnno.getType().getName());

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