Java Code Examples for org.apache.uima.cas.CAS#getLowLevelCAS()

public static Map<FeatureStructure, FeatureStructure> getNonIndexedFSesWithOwner(CAS aCas)
{
    TypeSystem ts = aCas.getTypeSystem();
    
    LowLevelCAS llcas = aCas.getLowLevelCAS();

    Set<FeatureStructure> allIndexedFS = collectIndexed(aCas);
    Map<FeatureStructure, FeatureStructure> allReachableFS = new TreeMap<>(
        Comparator.comparingInt(llcas::ll_getFSRef));
    
    FSIterator<FeatureStructure> i = aCas.getIndexRepository().getAllIndexedFS(
            aCas.getTypeSystem().getTopType());

    i.forEachRemaining(fs -> collect(allReachableFS, allIndexedFS, fs, fs));

    // Remove all that are not annotations
    allReachableFS.entrySet().removeIf(e -> 
            !ts.subsumes(aCas.getAnnotationType(), e.getKey().getType()));
    
    // Remove all that are indexed
    allReachableFS.entrySet().removeIf(e -> e.getKey() == e.getValue());

    // All that is left are non-index annotations
    return allReachableFS;
}
 

public static void deserialize(InputSource aSource, CAS aCAS, boolean aLenient)
    throws SAXException, IOException {

  XMLReader xmlReader = XMLUtils.createXMLReader();
  XCASDeserializer deser = new XCASDeserializer(aCAS.getTypeSystem());
  ContentHandler handler;
  if (aLenient) {
    handler = deser.getXCASHandler(aCAS, new OutOfTypeSystemData());
  } else {
    handler = deser.getXCASHandler(aCAS);
  }
  xmlReader.setContentHandler(handler);
  xmlReader.parse(aSource);

  CASImpl casImpl = ((CASImpl) aCAS.getLowLevelCAS());
  if (casImpl.is_ll_enableV2IdRefs()) {
    TOP highest_fs = ((XCASDeserializerHandler) handler).highestIdFs;

    casImpl.setLastUsedFsId(highest_fs._id);
    casImpl.setLastFsV2Size(highest_fs._getTypeImpl().getFsSpaceReq(highest_fs));
  }
}
 

public static Set<FeatureStructure> collectIndexed(CAS aCas)
{
    LowLevelCAS llcas = aCas.getLowLevelCAS();
    Set<FeatureStructure> fses = new TreeSet<>(Comparator.comparingInt(llcas::ll_getFSRef));

    FSIterator<FeatureStructure> i = aCas.getIndexRepository().getAllIndexedFS(
            aCas.getTypeSystem().getTopType());

    i.forEachRemaining(fses::add);

    return fses;
}
 

public static Set<FeatureStructure> collectReachable(CAS aCas)
{
    LowLevelCAS llcas = aCas.getLowLevelCAS();
    Set<FeatureStructure> fses = new TreeSet<>(Comparator.comparingInt(llcas::ll_getFSRef));

    FSIterator<FeatureStructure> i = aCas.getIndexRepository().getAllIndexedFS(
            aCas.getTypeSystem().getTopType());

    i.forEachRemaining(fs -> collect(fses, fs));

    return fses;
}
 

/**
 * Change from https://issues.apache.org/jira/browse/UIMA-3112 :
 *   requires that the CAS returned from the getLowLevelCAS() be castable to CASImpl
 * @param c1 -
 * @param c2 -
 * @return true if both views are in the same CAS (e.g., they have the same base CAS)
 */
private boolean casViewsInSameCas(CAS c1, CAS c2) {
  if (null == c1 || null == c2) {
    return false;
  }

  CASImpl ci1 = (CASImpl) c1.getLowLevelCAS();
  CASImpl ci2 = (CASImpl) c2.getLowLevelCAS();
  
  return ci1.getBaseCAS() == ci2.getBaseCAS();
}
 

private FeatureStructure createFS(CAS cas, Type type) {
  if (isKeep) {
    LowLevelCAS llCas = cas.getLowLevelCAS();
    return llCas.ll_getFSForRef(llCas.ll_createFS(((TypeImpl)type).getCode()));
  }
  return cas.createFS(type);
}
 

private TOP createArray(CAS cas, Type type, int length) {
  if (isKeep) {
    LowLevelCAS llCas = cas.getLowLevelCAS();
    return llCas.ll_getFSForRef(llCas.ll_createArray(((TypeImpl)type).getCode(), length));
  }
  return ((CASImpl)cas).createArray((TypeImpl)type, length);
}
 

private void setTokenAnnos(CAS aCas, Map<Integer, String> aTokenAnnoMap, Type aType,
        Feature aFeature)
{
    LowLevelCAS llCas = aCas.getLowLevelCAS();
    for (AnnotationFS annoFs : CasUtil.select(aCas, aType)) {
        boolean first = true;
        boolean previous = false; // exists previous annotation, place-holed O-_ should be kept
        for (Token token : selectCovered(Token.class, annoFs)) {
            if (annoFs.getBegin() <= token.getBegin() && annoFs.getEnd() >= token.getEnd()) {
                String annotation = annoFs.getFeatureValueAsString(aFeature);
                if (annotation == null) {
                    annotation = aType.getName() + "_";
                }
                if (aTokenAnnoMap.get(llCas.ll_getFSRef(token)) == null) {
                    if (previous) {
                        if (!multipleSpans.contains(aType.getName())) {
                            aTokenAnnoMap.put(llCas.ll_getFSRef(token), annotation);
                        }
                        else {
                            aTokenAnnoMap.put(llCas.ll_getFSRef(token), "O-_|"
                                    + (first ? "B-" : "I-") + annotation);
                            first = false;
                        }
                    }
                    else {
                        if (!multipleSpans.contains(aType.getName())) {
                            aTokenAnnoMap.put(llCas.ll_getFSRef(token), annotation);
                        }
                        else {
                            aTokenAnnoMap.put(llCas.ll_getFSRef(token), (first ? "B-" : "I-")
                                    + annotation);
                            first = false;
                        }
                    }
                }
                else {
                    if (!multipleSpans.contains(aType.getName())) {
                        aTokenAnnoMap.put(llCas.ll_getFSRef(token),
                                aTokenAnnoMap.get(llCas.ll_getFSRef(token)) + "|"
                                        + annotation);
                        previous = true;
                    }
                    else {
                        aTokenAnnoMap.put(llCas.ll_getFSRef(token),
                                aTokenAnnoMap.get(llCas.ll_getFSRef(token)) + "|"
                                        + (first ? "B-" : "I-") + annotation);
                        first = false;
                        previous = true;
                    }
                }

            }
        }
    }
}
 

public SelectFSs_impl(CAS cas) {
  this.view = (CASImpl) cas.getLowLevelCAS();
  this.jcas = (JCasImpl) view.getJCas();
}
 

public final static boolean isSameCAS(CAS c1, CAS c2) {
  CASImpl ci1 = (CASImpl) c1.getLowLevelCAS();
  CASImpl ci2 = (CASImpl) c2.getLowLevelCAS();
  return ci1.getBaseCAS() == ci2.getBaseCAS();
}
 

/**
   * Creates a new CasCopier that can be used to copy FeatureStructures from one CAS to another.
   * Note that if you are merging data from multiple CASes, you must create a new CasCopier
   * for each source CAS. This version of the constructor supports a "lenient copy" option. When set,
   * the CAS copy function will ignore (not attempt to copy) FSs and features not defined in the type system
   * of the destination CAS, rather than throwing an exception.
   * 
   * @param aSrcCas
   *          the CAS to copy from.
   * @param aDestCas
   *          the CAS to copy into.
   * @param lenient
   *          ignore FSs and features not defined in the type system of the destination CAS
   */
  public CasCopier(CAS aSrcCas, CAS aDestCas, boolean lenient) {

    mFsMap = new IdentityHashMap<>(((CASImpl)(aSrcCas.getLowLevelCAS())).getLastUsedFsId());
    originalSrcCas = (CASImpl)aSrcCas.getLowLevelCAS();
    originalTgtCas = (CASImpl)aDestCas.getLowLevelCAS();
    
    srcTsi = originalSrcCas.getTypeSystemImpl();
    tgtTsi = originalTgtCas.getTypeSystemImpl();

    src2TgtType = (srcTsi == tgtTsi) ? null : new Int2ObjListMap<>(srcTsi.getTypeArraySize());
    src2TgtFeat = (srcTsi == tgtTsi) ? null : new Int2ObjListMap<>(srcTsi.getNumberOfFeatures() + 1);
    

//    tInfoArray = new TypeInfo[srcTsi.getLargestTypeCode() + 1];
    
//    srcStringType = srcTsi.stringType;
//    srcStringTypeCode = srcStringType.getCode();
    
//    mDestSofaFeature = aDestCas.getTypeSystem().getFeatureByFullName(CAS.FEATURE_FULL_NAME_SOFA);
    this.lenient = lenient;
    
    // the next is to support the style of use where
    //   an instance of this copier is made, corresponding to two views in the same CAS
    //   or corresponding to two views in different CASs
    //   and then individual FeatureStructures are copied using copyFS(...)
    
    srcCasViewImpl = (CASImpl) originalSrcCas.getLowLevelCAS();
    tgtCasViewImpl = (CASImpl) originalTgtCas.getLowLevelCAS();
    
    srcViewName = srcCasViewImpl.getViewName();
    tgtViewName = tgtCasViewImpl.getViewName();
    
    if (srcViewName == null) {  // base cas
      isChangeViewName = (tgtViewName == null) ? false : true;
    } else {
      isChangeViewName = !srcViewName.equals(tgtViewName);
    }
    
    isEqualTypeSystems = srcTsi.equals(tgtTsi);
  }