Examples of 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.

Examples of org.apache.uima.cas.FSIterator

      FeatureStructure f1 = localCas.createFS(subTok);
      localCas.getIndexRepository().addFS(f1);


      JFSIndexRepository ir = jcas.getJFSIndexRepository();
      FSIndex index = ir.getAnnotationIndex();
      FSIterator it = index.iterator();


      try {


        while (it.isValid()) {
          Object o = it.get();
          assertTrue(o instanceof Annotation);
          it.moveToNext();
        }
      } catch (Exception e) {
        System.out.println("failed: nonJCasCovered by JCas");
      }
    } catch (Exception e) {

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Examples of org.apache.uima.cas.FSIterator


  public void testIteratorGetsJCasType() throws Exception {
    try {
      Token tok1 = new Token(jcas);
      tok1.addToIndexes();
      FSIterator it = jcas.getJFSIndexRepository().getIndex("all", Token.type).iterator();
      while (it.hasNext()) {
        Token token = (Token) it.next();
        token.addToIndexes(); // something to do to keep Java from optimizing this away.
      }
    } catch (Exception e) {
      JUnitExtension.handleException(e);
    }

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Examples of org.apache.uima.cas.FSIterator


    // 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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Examples of org.apache.uima.cas.FSIterator

      FSIndex engIndex = indexes.getAnnotationIndex(Annotation.type);
      indexes = gerJcas.getJFSIndexRepository();
      FSIndex gerIndex = indexes.getAnnotationIndex(Annotation.type);
      indexes = frJcas.getJFSIndexRepository();
      FSIndex frIndex = indexes.getAnnotationIndex(Annotation.type);
      FSIterator sofaIter = jcas.getSofaIterator();
      int numSofas = 0;
      while (sofaIter.isValid()) {
        numSofas++;
        sofaIter.moveToNext();
      }
      // assertTrue(sofaIndex.size() == 3); // 3 sofas
      assertTrue(numSofas == 3);
      assertTrue(engIndex.size() == 5); // 4 annots plus documentAnnotation
      assertTrue(gerIndex.size() == 5); // 4 annots plus documentAnnotation
      assertTrue(frIndex.size() == 5); // 4 annots plus documentAnnotation


      // Test that the annotations are of the correct types
      FSIterator engIt = engIndex.iterator();
      FSIterator gerIt = gerIndex.iterator();
      FSIterator frIt = frIndex.iterator();
      Annotation engAnnot = (Annotation) engIt.get();
      Annotation gerAnnot = (Annotation) gerIt.get();
      Annotation frAnnot = (Annotation) frIt.get();
      assertTrue((CAS.TYPE_NAME_DOCUMENT_ANNOTATION).equals(engAnnot.getType().getName()));
      assertTrue((CAS.TYPE_NAME_DOCUMENT_ANNOTATION).equals(gerAnnot.getType().getName()));
      assertTrue((CAS.TYPE_NAME_DOCUMENT_ANNOTATION).equals(frAnnot.getType().getName()));


      engIt.moveToNext();
      gerIt.moveToNext();
      frIt.moveToNext();
      engAnnot = (Annotation) engIt.get();
      CrossAnnotation gerCrossAnnot = (CrossAnnotation) gerIt.get();
      frAnnot = (Annotation) frIt.get();
      assertTrue((CAS.TYPE_NAME_ANNOTATION).equals(engAnnot.getType().getName()));
      assertTrue(("this").equals(engAnnot.getCoveredText()));
      assertTrue((CAS.TYPE_NAME_ANNOTATION).equals(frAnnot.getType().getName()));
      assertTrue(("cette").equals(frAnnot.getCoveredText()));
      assertTrue(("org.apache.uima.cas.test.CrossAnnotation").equals(gerCrossAnnot.getType()

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Examples of org.apache.uima.cas.FSIterator

    if (mTEXT) {
      // get the default View if it exists
      try {
        jcas = aCAS.getView(CAS.NAME_DEFAULT_SOFA).getJCas();
        hasDefaultView = true;
        FSIterator it = jcas.getAnnotationIndex(SourceDocumentInformation.type).iterator();
        if (it.hasNext()) {
          // get the output file name from the annotation in the CAS ...
          // ... note this is a little flakey if processing an XCAS file,
          // which could have such an annotation with a different name than the input XCAS file!
          // So we don't do this if XCAS output is specified.
          SourceDocumentInformation fileLoc = (SourceDocumentInformation) it.next();
          File inFile;
          inFile = new File(new URL(fileLoc.getUri()).getPath());
          outFile = new File(mOutputDir, inFile.getName());
        }
      } catch (CASRuntimeException e) {

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Examples of org.apache.uima.cas.FSIterator

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


    // retrieve 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 {
        // handle blanks in path
        // https://issues.apache.org/jira/browse/UIMA-1748
        // use 3 arg form of URI Constructor to properly quote any otherwise illegal chars such as blank

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Examples of org.apache.uima.cas.FSIterator

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


    // retrieve 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 {
        // handle blanks in path
        // https://issues.apache.org/jira/browse/UIMA-1748
        // use 3 arg form of URI Constructor to properly quote any otherwise illegal chars such as blank

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Examples of org.apache.uima.cas.FSIterator

    int end = whiskRuleItem.getWordConstraint().getTokenAnnotation().getEnd();
    CAS cas = example.getDocumentCAS();
    // TODO: access type with string constant
    Type frameType = cas.getTypeSystem().getType("org.apache.uima.ruta.type.RutaFrame");
    AnnotationFS pointer = cas.createAnnotation(frameType, end, Integer.MAX_VALUE);
    FSIterator iterator = cas.getAnnotationIndex().iterator(pointer);
    int nextBegin = -1;
    while (iterator.isValid()) {
      FeatureStructure fs = iterator.get();
      if (fs instanceof AnnotationFS) {
        AnnotationFS a = (AnnotationFS) fs;
        if (!filterSetWithSlotNames.contains(a.getType().getName())) {
          if (nextBegin == -1) {
            nextBegin = a.getBegin();
          } else if (nextBegin != a.getBegin()) {
            break;
          }
          if (a.getBegin() <= nextBegin && a.getBegin() >= end) {
            WhiskRuleItem term = new WhiskRuleItem(new TextRulerAnnotation(a,
                    example.getDocument(), consideredFeatures));
            result.add(term);
          }
        }
      }
      iterator.moveToNext();
    }
    return result;
  }

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Examples of org.apache.uima.cas.FSIterator

    CAS cas = example.getDocumentCAS();


    // TODO: access type with string constant
    Type frameType = cas.getTypeSystem().getType("org.apache.uima.ruta.type.RutaFrame");
    AnnotationFS pointer = cas.createAnnotation(frameType, begin, begin);
    FSIterator iterator = cas.getAnnotationIndex().iterator(pointer);
    int nextEnd = -1;


    // ???
    iterator.moveToPrevious();
    iterator.moveToPrevious();
    while (iterator.isValid()) {
      FeatureStructure fs = iterator.get();
      if (fs instanceof AnnotationFS) {
        AnnotationFS a = (AnnotationFS) fs;
        if (!filterSetWithSlotNames.contains(a.getType().getName())) {
          if (a.getEnd() > example.getAnnotation().getEnd()) {
            iterator.moveToPrevious();
            continue;
          }
          if (nextEnd == -1) {
            nextEnd = a.getEnd();
          } else if (nextEnd != a.getEnd()) {
            break;
          }
          if (a.getEnd() >= nextEnd && a.getEnd() <= begin) {
            WhiskRuleItem term = new WhiskRuleItem(new TextRulerAnnotation(a,
                    example.getDocument(), consideredFeatures));
            result.add(term);
          }
        }
      }
      iterator.moveToPrevious();
    }
    return result;
  }

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Examples of org.apache.uima.cas.FSIterator

    List<List<WhiskRuleItem>> result = new ArrayList<List<WhiskRuleItem>>();
    CAS cas = example.getDocumentCAS();
    // TODO: access type with string constant
    Type frameType = cas.getTypeSystem().getType("org.apache.uima.ruta.type.RutaFrame");
    AnnotationFS pointer = cas.createAnnotation(frameType, startPos, endPos);
    FSIterator iterator = cas.getAnnotationIndex().iterator(pointer);
    List<AnnotationFS> startAs = new ArrayList<AnnotationFS>();
    int firstBegin = -1;
    while (iterator.isValid()) {
      FeatureStructure fs = iterator.get();
      AnnotationFS a = (AnnotationFS) fs;


      // TODO change for multislot rules!
      if (a.getBegin() >= startPos && a.getEnd() <= endPos) {
        if (!filterSetWithSlotNames.contains(a.getType().getName())) {
          if (firstBegin == -1) {
            firstBegin = a.getBegin();
          } else if (firstBegin != a.getBegin()) {
            break;
          }
          if (a.getBegin() == firstBegin)
            startAs.add(a);
        }
        iterator.moveToNext();
      } else {
        iterator.moveToNext();
      }
    }


    for (AnnotationFS annotation : startAs) {
      List<WhiskRuleItem> startList = new ArrayList<WhiskRuleItem>();

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