/*
 * Copyright (c) 2009 Peter Troshin JAva Bioinformatics Analysis Web Services
 * (JABAWS) @version: 1.0 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.runner.disorder;

import java.util.Arrays;
import java.util.Map;

import org.apache.log4j.Logger;

import compbio.data.sequence.Score;
import compbio.engine.client.Executable;
import compbio.engine.client.PipedExecutable;
import compbio.engine.client.SkeletalExecutable;
import compbio.metadata.Limit;
import compbio.metadata.LimitsManager;
import compbio.metadata.ResultNotAvailableException;
import compbio.runner.Util;

/**
 * @see DisEMBL
 * 
 *      DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops
 *      fold_rem465 sequence_file print 'A default run would be: ./DisEMBL.py 8
 *      8 4 1.2 1.4 1.2 fasta_file > out' new DisEMBL is at
 *      /homes/pvtroshin/soft/DisEMBL-1.4raw
 * 
 *      This is not a standard DisEMBL! The script has been modified! DisEMBL.py
 *      smooth_frame peak_frame join_frame fold_coils fold_hotloops fold_rem465
 *      [mode] < fasta_file > out print
 * 
 *      'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 < fasta_file'
 *      print 'Mode: "default"(nothing) or "scores" which will give scores per
 *      residue in TAB separated format'
 */
public class Disembl extends SkeletalExecutable<Disembl>
		implements
			PipedExecutable<Disembl> {

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

	// Cache for Limits information
	private static LimitsManager<Disembl> limits;

	public static final String KEY_VALUE_SEPARATOR = Util.SPACE;

	public Disembl() {
		// remove default input to prevent it to appear in the parameters list
		// that could happen if the parameters are set first
		// super.setInput("");
		addParameters(Arrays.asList("8", "8", "4", "1.2", "1.4", "1.2",
				"scores"));
	}

	@SuppressWarnings("unchecked")
	public Map<String, Score> getResults(String workDirectory)
			throws ResultNotAvailableException {

		return null;
	}

	@Override
	public Disembl setInput(String inFile) {
		super.setInput(inFile);
		cbuilder.setLast(inFile);
		return this;
	}

	@Override
	public Limit<Disembl> getLimit(String presetName) {
		if (limits == null) {
			limits = getLimits();
		}

		Limit<Disembl> limit = null;
		if (limits != null) {
			// this returns default limit if preset is undefined!
			limit = limits.getLimitByName(presetName);
		}
		// If limit is not defined for a particular preset, then return default
		// limit
		if (limit == null) {
			log.debug("Limit for the preset " + presetName
					+ " is not found. Using default");
			limit = limits.getDefaultLimit();
		}
		return limit;
	}

	@Override
	public LimitsManager<Disembl> getLimits() {
		// synchronise on static field
		synchronized (log) {
			if (limits == null) {
				limits = Util.getLimits(this.getClass());
			}
		}
		return limits;
	}

	@Override
	public Class<? extends Executable<?>> getType() {
		return this.getClass();
	}

}