package compbio.ws.server;

import java.io.File;
import java.util.Arrays;
import java.util.List;

import javax.jws.WebService;

import org.apache.log4j.Logger;

import compbio.data.msa.SequenceAnnotation;
import compbio.data.sequence.FastaSequence;
import compbio.engine.Configurator;
import compbio.engine.client.ConfiguredExecutable;
import compbio.metadata.ChunkHolder;
import compbio.metadata.JobSubmissionException;
import compbio.metadata.LimitExceededException;
import compbio.metadata.UnsupportedRuntimeException;
import compbio.runner.conservation.AACon;

@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "AAConWS")
public class AAConWS extends SequenceAnnotationService<AACon>
		implements
			SequenceAnnotation<AACon> {

	private static Logger log = Logger.getLogger(AAConWS.class);

	public AAConWS() {
		super(new AACon(), log);
	}

	/*
	 * @SuppressWarnings("unchecked") public JalviewAnnotation
	 * getJalviewAnnotation(String jobId) throws ResultNotAvailableException {
	 * MultiAnnotatedSequence<Method> result = getResult(jobId); // TODO //
	 * log(jobId, "getResults"); return result.toJalviewAnnotation(); }
	 */

	@Override
	public String analize(List<FastaSequence> sequences)
			throws UnsupportedRuntimeException, LimitExceededException,
			JobSubmissionException {
		WSUtil.validateAAConInput(sequences);
		ConfiguredExecutable<AACon> confAAcon = init(sequences);

		// set default conservation method to fastest - SHENKIN
		// TODO: This violates encapsulation, should be moved to the runners
		// level.
		confAAcon.addParameters(Arrays.asList("-m=SHENKIN"));
		return WSUtil.analize(sequences, confAAcon, log, "AAConWS analize",
				getLimit(""));
	}

	@Override
	public ChunkHolder pullExecStatistics(String jobId, long position) {
		WSUtil.validateJobId(jobId);
		String file = Configurator.getWorkDirectory(jobId) + File.separator
				+ AACon.getStatFile();
		return WSUtil.pullFile(file, position);
	}

}