/* Copyright (c) 2013 Alexander Sherstnev
 *  
 *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 3.0     
 * 
 *  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.predictors;

import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.util.Arrays;
import java.util.List;

import org.apache.log4j.Logger;

import compbio.data.sequence.JpredAlignment;
import compbio.data.sequence.AlignmentMetadata;
import compbio.data.sequence.Program;
import compbio.data.sequence.SequenceUtil;
import compbio.engine.client.CommandBuilder;
import compbio.engine.client.Executable;
import compbio.engine.client.SkeletalExecutable;
import compbio.metadata.ResultNotAvailableException;

/**
 * Command line
 * 
 * jpred.pl -in d16vpa_.fas -outfile res_d16vpa_ -dbname ported_db -dbpath
 * /data/UNIREFdb -ncpu 4
 * 
 * @author asherstnev
 * 
 */
public class Jpred extends SkeletalExecutable<Jpred> {

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

	/**
	 * Number of cores to use, defaults to 1 for local execution or the value of
	 * "jpred.cluster.cpunum" property for cluster execution
	 */
	private int ncoreNumber = 0;

	public static final String KEY_VALUE_SEPARATOR = " ";
	public static final String STAT_FILE = "stat.txt";

	public Jpred() {
		String dbpath = ph.getProperty("jpred.data.uniref.path");
		String dbname = ph.getProperty("jpred.data.uniref.name");
		addParameters(Arrays.asList("-logfile " + STAT_FILE));
		addParameters(Arrays.asList("-dbpath " + dbpath));
		addParameters(Arrays.asList("-dbname " + dbname));
		addParameters(Arrays.asList("-jabaws"));
	}

	// HashMap<Method, float[]>
	@SuppressWarnings("unchecked")
	@Override
	public JpredAlignment getResults(String workDirectory) throws ResultNotAvailableException {
		JpredAlignment annotations = null;
		try {
			InputStream inStream = new FileInputStream(new File(workDirectory, getOutput()));
			annotations = new JpredAlignment(SequenceUtil.readJpredFile(inStream), new AlignmentMetadata(Program.Jpred, '-'));
		} catch (FileNotFoundException e) {
			log.error(e.getMessage(), e.getCause());
			throw new ResultNotAvailableException(e);
		} catch (IOException e) {
			log.error(e.getMessage(), e.getCause());
			throw new ResultNotAvailableException(e);
		} catch (NullPointerException e) {
			log.error(e.getMessage(), e.getCause());
			throw new ResultNotAvailableException(e);
		}
		return annotations;
	}

	@Override
	public List<String> getCreatedFiles() {
		return Arrays.asList(getOutput(), getError());
	}

	@Override
	public Jpred setInput(String inFile) {
		super.setInput(inFile);
		cbuilder.setParam("-in " + inFile);
		return this;
	}

	@Override
	public Jpred setOutput(String outFile) {
		super.setOutput(outFile);
		cbuilder.setParam("-outfile " + outFile);
		return this;
	}

	@SuppressWarnings("unchecked")
	@Override
	public Class<Jpred> getType() {
		return (Class<Jpred>) this.getClass();
	}

	public static String getStatFile() {
		return STAT_FILE;
	}

	public void setNCore(int ncoreNumber) {
		if (0 < ncoreNumber && ncoreNumber < 9) {
			this.ncoreNumber = ncoreNumber;
			cbuilder.setParam("-ncpu " + Integer.toString(getNCore()));
		} else {
			throw new IndexOutOfBoundsException("Number of cores must be between 1 and 8 ");
		}
	}

	int getNCore() {
		return ncoreNumber;
	}

	@Override
	public CommandBuilder<Jpred> getParameters(ExecProvider provider) {
		// If number of cores is provided, set it for the cluster execution
		// only!
		if (provider == Executable.ExecProvider.Cluster) {
			int cpunum = SkeletalExecutable.getClusterCpuNum(getType());
			cpunum = (cpunum == 0) ? 1 : cpunum;
			setNCore(cpunum);
		} else {
			// Limit number of cores to 1 for ANY execution which does not set
			// Ncores explicitly using setNCore method or is run on local VM
			if (ncoreNumber == 0) {
				setNCore(1);
			}
		}
		return super.getParameters(provider);
	}

}