Examples of org.apache.uima.jcas.tcas.Annotation

org.apache.uima.jcas.tcas.Annotation
the JCas class model for the CAS type uima.cas.Annotation. It defines two integer valued features indicating the begin and end of the span being annotated. There is also a method to retrieve the spanned text as a string.

  public void testGetAllAnnotationsOfCustomType() {
    try {
      JCas cas = getCAS().getJCas();
      cas.setDocumentText(DOCUMENT_TEXT);


      Annotation simpleAnnotation = new Annotation(cas);
      simpleAnnotation.setBegin(10);
      simpleAnnotation.setEnd(24);
      simpleAnnotation.addToIndexes();


      Annotation secondSimpleAnnotation = new Annotation(cas);
      secondSimpleAnnotation.setBegin(32);
      secondSimpleAnnotation.setEnd(44);
      secondSimpleAnnotation.addToIndexes();


      List<Annotation> foundAnnotations = UIMAUtils.getAllAnnotationsOfType(DocumentAnnotation.type, cas);


      assertTrue(foundAnnotations != null);
      assertTrue(!foundAnnotations.isEmpty());

View Full Code Here

    } catch (CASException e) {
      throw new RuntimeException(e);
    }
    FSIterator iter = jcas.getAnnotationIndex().iterator();
    while (iter.isValid()) {
      Annotation annot = (Annotation) iter.get();
      iter.moveToNext();


      // find out what entity this annotation represents
      EntityResolver.Entity entity = mEntityResolver.getEntity(annot);


      //if not an entity, skip it
      if (entity == null)
        continue;
      
      // have we seen this entity before?
      JCheckBox checkbox = (JCheckBox) mEntityToCheckboxMap.get(entity);
      if (checkbox == null) {
        // assign next available color
        Color c = COLORS[mEntityToCheckboxMap.size() % COLORS.length];
        // add checkbox
        checkbox = new JCheckBox(entity.getCanonicalForm(), true);
        checkbox.setToolTipText(entity.getCanonicalForm());
        checkbox.addActionListener(this);
        checkbox.setBackground(c);
        entityCheckboxPanel.add(checkbox);
        // add to (Entity, Checkbox) map
        mEntityToCheckboxMap.put(entity, checkbox);
      }


      // if checkbox is checked, assign color to text
      if (checkbox.isSelected()) {
        int begin = annot.getBegin();
        int end = annot.getEnd();
        // be careful of 0-length annotation. If we try to set background color when there
        // is no selection, it will set the input text style, which is not what we want.
        if (begin != end) {
          MutableAttributeSet attrs = new SimpleAttributeSet();
          StyleConstants.setBackground(attrs, checkbox.getBackground());

View Full Code Here

      JUnitExtension.handleException(e);
    }
  }


  public void testIteratorCopy() {
    Annotation something = new Annotation(jcas);
    something.addToIndexes();


    JFSIndexRepository ir = jcas.getJFSIndexRepository();
    FSIterator i1 = ir.getAnnotationIndex().iterator();
    FSIterator i2 = i1.copy();
    FSIterator i3 = i2.copy();

View Full Code Here

      TOP_Type type = jcas.getType(org.apache.uima.jcas.tcas.Annotation.type);
      assertTrue(type instanceof org.apache.uima.jcas.tcas.Annotation_Type);
      type = jcas.getType(Annotation.typeIndexID);
      assertTrue(type instanceof Annotation_Type);


      Annotation a1 = new Annotation(jcas, 4, 5);
    } catch (Exception e) {
      JUnitExtension.handleException(e);
    }
  }

View Full Code Here


  public void testNonJCasCoveredByJCas() throws Exception {
    try {
      CAS localCas = jcas.getCas();
      Type subTok = localCas.getTypeSystem().getType("SubToken");
      Annotation a1 = new Annotation(jcas);
      a1.addToIndexes();
      FeatureStructure f1 = localCas.createFS(subTok);
      localCas.getIndexRepository().addFS(f1);


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

View Full Code Here

    }
    //check that this does not leave JCAS in an inconsistent state
    //(a check for bug UIMA-738)
    Iterator<Annotation> iter = jcas.getAnnotationIndex().iterator();
    assertTrue(iter.hasNext());
    Annotation annot = iter.next();
    assertEquals("This is a test.", annot.getCoveredText());
  }

View Full Code Here


        String fTok = fst.nextToken();
        int frBegin = frText.indexOf(fTok, frEnd);
        frEnd = frBegin + fTok.length();


        Annotation engAnnot = new Annotation(engJcas, engBegin, engEnd);
        engAnnot.addToIndexes();


        Annotation frAnnot = new Annotation(frJcas, frBegin, frEnd);
        frAnnot.addToIndexes();


        CrossAnnotation gerAnnot = new CrossAnnotation(gerJcas);
        gerAnnot.setBegin(gerBegin);
        gerAnnot.setEnd(gerEnd);
        gerAnnot.setOtherAnnotation(engAnnot);
        gerAnnot.addToIndexes();
      }


      // Test that the annotations are in separate index spaces, and that Sofas are indexed
      JFSIndexRepository indexes = jcas.getJFSIndexRepository();
      // FSIndex sofaIndex = indexes.getIndex(CAS.SOFA_INDEX_NAME);
      indexes = engJcas.getJFSIndexRepository();
      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()
              .getName()));
      assertTrue(("das").equals(gerCrossAnnot.getCoveredText()));


      // Test that the other annotation feature of cross annotations works
      Annotation crossAnnot = gerCrossAnnot.getOtherAnnotation();
      assertTrue((CAS.TYPE_NAME_ANNOTATION).equals(crossAnnot.getType().getName()));
      assertTrue(("this").equals(crossAnnot.getCoveredText()));


      // Test that annotations accessed from a reference in the base CAS work correctly
      FSArray anArray = new FSArray(jcas, 3);
      anArray.set(0, engAnnot);
      anArray.set(1, frAnnot);
      anArray.set(2, gerCrossAnnot);
      Annotation tstAnnot = (Annotation) anArray.get(0);
      assertTrue(("this").equals(tstAnnot.getCoveredText()));
      tstAnnot = (Annotation) anArray.get(1);
      assertTrue(("cette").equals(tstAnnot.getCoveredText()));
      tstAnnot = (Annotation) anArray.get(2);
      assertTrue(("das").equals(tstAnnot.getCoveredText()));
    } catch (Exception e) {
      JUnitExtension.handleException(e);
    }
  }

View Full Code Here

      CAS newCas = CasCreationUtils.createCas(new TypeSystemDescription_impl(), null, null);
      JCas newJCas = newCas.getJCas();
      CAS view = newCas.createView("DetaggedView");
      view.getJCas();


      Annotation annot = new Annotation(newJCas);
      annot.addToIndexes();
      
      Iterator<Annotation> annotIter = newJCas.getAnnotationIndex(Annotation.type).iterator();
      Annotation annot2 = annotIter.next();
      assertEquals(annot, annot2);
      assertEquals(annot2.getSofa(), annot2.getCASImpl().getSofa());
      
      annot2.addToIndexes();
    }
    catch (Exception e) {
      JUnitExtension.handleException(e);      
    }    
  }

View Full Code Here

      // TODO Auto-generated catch block
      e1.printStackTrace();
      assertTrue(false);
    }
    FSIndex jcasSetIndex = jcas.getJFSIndexRepository().getIndex(CASTestSetup.ANNOT_SET_INDEX);
    Annotation jcasAnnotation = (Annotation) jcasSetIndex.find(annot);
    assertNotNull(jcasAnnotation);
    assertNull(jcasSetIndex.find(this.cas.createAnnotation(this.annotationType, -1, -1)));


    // /////////////////////////////////////////////////////////////////////////
    // Test fast fail.

View Full Code Here

    this.jCas.setDocumentText("A B C");
    // remove the DocumentAnnotation
    for (Annotation ann : JCasUtil.select(jCas, Annotation.class)) {
      ann.removeFromIndexes();
    }
    Annotation a = new Annotation(this.jCas, 0, 1);
    Annotation b = new Annotation(this.jCas, 2, 3);
    Annotation c = new Annotation(this.jCas, 4, 5);
    for (Annotation ann : Arrays.asList(a, b, c)) {
      ann.addToIndexes();
    }


    assertEquals(Arrays.asList(a), selectPreceding(this.jCas, Annotation.class, b, 2));

View Full Code Here

0 1 2 3 4 5 6 7 8 9

TOP

Related Classes of org.apache.uima.jcas.tcas.Annotation

fr.univnantes.lina.uima.dictionaryAnnotator.DictionaryAnnotatorAE

org.apache.clerezza.uima.utils.UIMAUtilsTest

org.apache.ctakes.assertion.eval.AssertionEvalBasedOnModifier$ReplaceCTakesEntityMentionsAndModifiersWithGold

org.apache.ctakes.assertion.eval.AssertionEvalBasedOnModifier$ReplaceGoldEntityMentionsAndModifiersWithCTakes

org.apache.ctakes.assertion.eval.AssertionEvaluation

org.apache.ctakes.assertion.eval.AssertionEvaluation$ReplaceCTakesEntityMentionsAndModifiersWithGold

org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine

org.apache.ctakes.assertion.medfacts.i2b2.api.CharacterOffsetToLineTokenConverterCtakesImpl

org.apache.ctakes.assertion.medfacts.i2b2.api.SingleDocumentProcessorCtakes

org.apache.ctakes.core.ae.FilterAnnotator

All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.