/* Copyright (c) 2011 Peter Troshin
 *  
 *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     
 * 
 *  This library is free software; you can redistribute it and/or modify it under the terms of the
 *  Apache License version 2 as published by the Apache Software Foundation
 * 
 *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
 *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache 
 *  License for more details.
 * 
 *  A copy of the license is in apache_license.txt. It is also available here:
 * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
 * 
 * Any republication or derived work distributed in source code form
 * must include this copyright and license notice.
 */
package compbio.ws.server;

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

import org.apache.log4j.Logger;

import compbio.data.sequence.Alignment;
import compbio.data.sequence.FastaSequence;
import compbio.engine.AsyncExecutor;
import compbio.engine.Configurator;
import compbio.engine.client.ConfiguredExecutable;
import compbio.engine.client.SkeletalExecutable;
import compbio.metadata.ChunkHolder;
import compbio.metadata.JobSubmissionException;
import compbio.metadata.Limit;
import compbio.metadata.Option;
import compbio.metadata.Preset;
import compbio.metadata.ResultNotAvailableException;
import compbio.metadata.WrongParameterException;
import compbio.runner.msa.ClustalW;

/**
 * 
 * TODO to complete after the approach is tested with SequenceAnnotation!
 * 
 * Common methods for all SequenceAnnotation web services
 * 
 * @author pvtroshin
 * 
 * @param <T>
 * 
 * @version 1.0 June 2011
 * @since 2.0
 */
public abstract class _MsaService<T> extends GenericMetadataService {

	/*
	 * FIXME - instances of the Runner (?) and their types should be defined in
	 * Executable IF
	 */
	_MsaService(SkeletalExecutable<T> exec, Logger log) {
		super(exec, log);
	}

	public String align(List<FastaSequence> sequences)
			throws JobSubmissionException {

		WSUtil.validateFastaInput(sequences);
		ConfiguredExecutable<T> confClust = init(sequences);
		return WSUtil.align(sequences, confClust, log, "align", getLimit(""));
	}

	public String presetAlign(List<FastaSequence> sequences, Preset<T> preset)
			throws JobSubmissionException, WrongParameterException {
		WSUtil.validateFastaInput(sequences);
		if (preset == null) {
			throw new WrongParameterException("Preset must be provided!");
		}
		Limit<T> limit = getLimit(preset.getName());
		ConfiguredExecutable<T> confClust = init(sequences);
		confClust.addParameters(preset.getOptions());
		return WSUtil.align(sequences, confClust, log, "presetAlign", limit);
	}

	public String customAlign(List<FastaSequence> sequences,
			List<Option<T>> options) throws JobSubmissionException,
			WrongParameterException {
		WSUtil.validateFastaInput(sequences);
		ConfiguredExecutable<T> confClust = init(sequences);
		List<String> params = WSUtil.getCommands(options,
				ClustalW.KEY_VALUE_SEPARATOR);
		confClust.addParameters(params);
		log.info("Setting parameters: " + params);
		return WSUtil.align(sequences, confClust, log, "customAlign",
				getLimit(""));
	}

	@SuppressWarnings("unchecked")
	public Alignment getResult(String jobId) throws ResultNotAvailableException {

		WSUtil.validateJobId(jobId);
		AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
		ConfiguredExecutable<T> clustal = (ConfiguredExecutable<T>) asyncEngine
				.getResults(jobId);
		Alignment al = clustal.getResults();
		return al;
	}

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

}