public void process()

in ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/JointRelationTokenBasedAnnotator.java [91:242]
108 lines of code
28 McCabe index (conditional complexity)

	public void process(JCas jCas) throws AnalysisEngineProcessException {
		if(timexMode == OutputMode.IndexTags && !this.isTraining()){
			final String timexIdxMapFile = "target/eval/thyme/train_and_test/event-event/timex_idx.txt";
			try {
				timex_idx = TimexIdxReader(FileLocator.getAsStream(timexIdxMapFile));
			} catch (IOException e) {
				e.printStackTrace();
			}
		}

		//		Map<EventMention, Collection<EventMention>> coveringMap =
		//				JCasUtil.indexCovering(jCas, EventMention.class, EventMention.class);

		// get all gold relation lookup
		Map<List<Annotation>, BinaryTextRelation> relationLookup;
		relationLookup = new HashMap<>();
		if (this.isTraining()) {
			relationLookup = new HashMap<>();
			for (BinaryTextRelation relation : JCasUtil.select(jCas, BinaryTextRelation.class)) {
				Annotation arg1 = relation.getArg1().getArgument();
				Annotation arg2 = relation.getArg2().getArgument();
				// The key is a list of args so we can do bi-directional lookup
				List<Annotation> key = Arrays.asList(arg1, arg2);
				if(relationLookup.containsKey(key)){
					String reln = relationLookup.get(key).getCategory();
					System.err.println("Error in: "+ ViewUriUtil.getURI(jCas).toString());
					System.err.println("Error! This attempted relation " + relation.getCategory() + 
							" already has a relation " + reln + " at this span: " + 
							arg1.getCoveredText() + " -- " + arg2.getCoveredText());
				} else {
					relationLookup.put(key, relation);
				}
			}
		}

		for(Sentence sentence : JCasUtil.select(jCas, Sentence.class)) {
			// collect all relevant relation arguments from the sentence
			List<IdentifiedAnnotationPair> candidatePairs = getCandidateRelationArgumentPairs(jCas, sentence);

			// walk through the pairs of annotations
			for (IdentifiedAnnotationPair pair : candidatePairs) {
				IdentifiedAnnotation arg1 = pair.getArg1();
				IdentifiedAnnotation arg2 = pair.getArg2();

				String context;
				String cuis;
				if(arg2.getBegin() < arg1.getBegin()) {
					// ... event2 ... event1 ... scenario
					if(timexMode == OutputMode.TokenSeq){
						String arg2tag = "e2";
						if(arg2 instanceof TimeMention){
							arg2tag="t";
						}
						context = ArgContextProvider.getTokenContext(jCas, sentence, arg2, arg2tag, arg1, "e1", 2); 

					}else{
						context = getTokenTimexContext(jCas, sentence, arg2, "e2", arg1, "e1", 2);
					}
				} else {
					// ... event1 ... event2 ... scenario
					if(timexMode == OutputMode.TokenSeq){
						String arg2tag ="e2";
						if(arg2 instanceof TimeMention){
							arg2tag="t";
						}
						context = ArgContextProvider.getTokenContext(jCas, sentence, arg1, "e1", arg2, arg2tag, 2);
					}else{
						context = getTokenTimexContext(jCas, sentence, arg1, "e1", arg2, "e2", 2);
					}
				}

				//get CUIs for two arguments
				//				Set<String> CUIs = getCuiDtrel(jCas, arg1);
				//				CUIs.addAll(getCuiDtrel(jCas, arg2));
				//
				//				cuis = String.join(" ", CUIs);

				//derive features based on context:
				List<Feature> feats = new ArrayList<>();
				String[] tokens = context.split(" ");
				//				String[] tokens = (context + "|" + cuis).split(" ");
				for (String token: tokens){
					feats.add(new Feature(token.toLowerCase()));
				}

				// during training, feed the features to the data writer
				if(this.isTraining()) {
					String category = getRelationCategory(relationLookup, arg1, arg2);

					// drop some portion of negative examples during training
					// if(category == null && coin.nextDouble() <= 0.5) {
					//   continue; // skip this negative example
					// }

					if(category == null) {
						category = NO_RELATION_CATEGORY;
					} else{
						category = category.toLowerCase();
					}
					this.dataWriter.write(new Instance<>(category, feats));
				} else {
					String predictedCategory = this.classifier.classify(feats);

					// add a relation annotation if a true relation was predicted
					if (predictedCategory != null && !predictedCategory.equals(NO_RELATION_CATEGORY)) {

						// if we predict an inverted relation, reverse the order of the
						// arguments
						//if for event-time relations:
						if(arg1 instanceof TimeMention || arg2 instanceof TimeMention){
							if(predictedCategory.endsWith("-1")) {
								predictedCategory = predictedCategory.substring(0, predictedCategory.length() - 2);
								if(arg1 instanceof TimeMention){
									IdentifiedAnnotation temp = arg1;
									arg1 = arg2;
									arg2 = temp;
								}
							} else {
								if(arg1 instanceof EventMention){
									IdentifiedAnnotation temp = arg1;
									arg1 = arg2;
									arg2 = temp;
								}
							}

							//							createRelation(jCas, arg1, arg2, predictedCategory.toUpperCase(), 0.0);
						}else{//if for event-event relations:		
							if (predictedCategory.endsWith("-1")) {
								predictedCategory = predictedCategory.substring(0, predictedCategory.length() - 2);
								IdentifiedAnnotation temp = arg1;
								arg1 = arg2;
								arg2 = temp;
							}

							//							createRelation(jCas, arg1, arg2, predictedCategory.toUpperCase(), 0.0);
						}

						createRelation(jCas, arg1, arg2, predictedCategory.toUpperCase(), 0.0);
					}
				}
			}

		}
		if(timexMode== OutputMode.IndexTags && !this.isTraining()){//in test time update the hashmap file for each cas
			try {
				TimexIdxWriter();
			} catch (IOException e) {
				// TODO Auto-generated catch block
				e.printStackTrace();
			}
		}
	}