package oboannotator.annotator;

import java.util.Iterator;

import oboannotator.typesys.MedlineDocument;
import oboannotator.typesys.MedlineField;

import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
import org.apache.uima.cas.FSIndex;
import org.apache.uima.conceptMapper.DictTerm;
import org.apache.uima.conceptMapper.support.tokenizer.TokenAnnotation;
import org.apache.uima.jcas.JCas;



public class DataRecordAnnotator extends JCasAnnotator_ImplBase {

	/**
	 * @see JCasAnnotator_ImplBase#process(JCas)
	 */
	public void process(JCas aJCas) {
		// get annotation indexes
		FSIndex mlDocIndex = aJCas.getAnnotationIndex(MedlineDocument.type);
		FSIndex mlFieldIndex = aJCas.getAnnotationIndex(MedlineField.type);
		FSIndex tokenIndex = aJCas.getAnnotationIndex(TokenAnnotation.type);
		FSIndex dictTermIndex = aJCas.getAnnotationIndex(DictTerm.type);

		// store end position of last meeting we identified, to prevent multiple
		// annotations over same span
		//int lastMeetingEnd = -1;

		// iterate over all combinations
		Iterator mlDocIter = mlDocIndex.iterator();
		while (mlDocIter.hasNext()) {
			MedlineDocument mlDoc = (MedlineDocument) mlDocIter.next();
			System.out.println("Doc ID: " + mlDoc.getDocID());

			Iterator mlFieldIter = mlFieldIndex.iterator();
			while (mlFieldIter.hasNext()) {
				MedlineField mlField = (MedlineField) mlFieldIter.next();
				if("UI".equals(mlField.getName())){
					System.out.println("Document ID: " + mlField.getName());
					//mlField.getText()
				}
				
				Iterator tokenIter = tokenIndex.iterator();
				while (tokenIter.hasNext()) {
					TokenAnnotation tokenAnnot = (TokenAnnotation) tokenIter
							.next();

					Iterator dictTermIter = dictTermIndex.iterator();
					while (dictTermIter.hasNext()) {
						DictTerm dictTerm = (DictTerm) dictTermIter.next();

//						DataRecord dr = new DataRecord(aJCas, dictTerm
//								.getBegin(), dictTerm.getEnd(), mlDoc, mlField,
//								tokenAnnot, dictTerm);
						//System.out.println("Doc ID: " + mlDoc.getDocID());
						//System.out.println("Doc Text: " + mlDoc.getText());
//						System.out.println("Dict Covered Text: " + dictTerm.getCoveredText());
//						System.out.println("Dict Canon: " + dictTerm.getDictCanon());
//						System.out.println("Dict Matched Text: " + dictTerm.getMatchedText());
//						System.out.println("Dict Sofa: " + dictTerm.getSofa());
					}
				}
			}
		}
	}
}