BLOFindIslands.java

/*******************************************************************************
 * GenPlay, Einstein Genome Analyzer
 * Copyright (C) 2009, 2014 Albert Einstein College of Medicine
 * 
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 * 
 * This program 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
 * GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 * Authors: Julien Lajugie <julien.lajugie@einstein.yu.edu>
 *          Nicolas Fourel <nicolas.fourel@einstein.yu.edu>
 *          Eric Bouhassira <eric.bouhassira@einstein.yu.edu>
 * 
 * Website: <http://genplay.einstein.yu.edu>
 ******************************************************************************/
package edu.yu.einstein.genplay.core.operation.binList;

import java.util.concurrent.ExecutionException;

import edu.yu.einstein.genplay.core.operation.Operation;
import edu.yu.einstein.genplay.core.operation.binList.peakFinder.IslandFinder;
import edu.yu.einstein.genplay.dataStructure.enums.IslandResultType;
import edu.yu.einstein.genplay.dataStructure.list.genomeWideList.SCWList.binList.BinList;


/**
 * Use the Island approach to separate data on islands
 * @author Nicolas Fourel
 */
public class BLOFindIslands implements Operation<BinList[]> {

	private final BinList 		inputBinList;	// input binlist
	private BinList[]			outputBinList;	// result list
	private IslandResultType[] 	list;			// the types of result
	private final IslandFinder 	island;			// the island finder object


	/**
	 * @param binList
	 * @throws InterruptedException
	 * @throws ExecutionException
	 */
	public BLOFindIslands (BinList binList) throws InterruptedException, ExecutionException {
		inputBinList = binList;
		island = new IslandFinder(binList);
	}


	@Override
	public BinList[] compute () throws InterruptedException, ExecutionException, CloneNotSupportedException {
		outputBinList = new BinList[list.length];
		for (int i=0; i < list.length; i++) {
			if (list[i] != null) {
				island.setResultType(list[i]);	// at this point, the resultType setting is the last to set
				outputBinList[i] = island.findIsland();	// we store the calculated bin list on the output binlist array of bloIsland object
			}
		}
		return outputBinList;
	}


	@Override
	public String getDescription () {
		String description = "Operation: Island Finder";
		description += ", Window value: " + getIsland().getWindowLimitValue();
		description += ", Gap: " + getIsland().getGap();
		description += ", Island score: " + getIsland().getIslandLimitScore();
		description += ", Island length: " + getIsland().getMinIslandLength();
		//description += ", Result type: " + getIsland().getResultType();
		return description;
	}


	/**
	 * @return the {@link IslandFinder} object
	 */
	public IslandFinder getIsland() {
		return island;
	}


	@Override
	public String getProcessingDescription() {
		return "Searching Islands";
	}


	/**
	 * @return the result types of the operation
	 */
	public IslandResultType[] getResultTypes() {
		return list;
	}


	@Override
	public int getStepCount() {
		return (inputBinList.getCreationStepCount() + 1) * numResult();
	}


	/**
	 * Count the number of valid result type.
	 * The array size will be always 2 (filtered & island score) but some fields can be null and do not been counted.
	 * @return	number of valid result type
	 */
	private int numResult() {
		int cpt = 0;
		for (int i=0; i < list.length; i++) {
			if (list[i] != null) {
				cpt++;
			}
		}
		return cpt;
	}


	/**
	 * @param list an array containing the result types of the operation
	 */
	public void setList(IslandResultType[] list) {
		this.list = list;
	}


	@Override
	public void stop() {
		if (island != null) {
			island.stop();
		}
	}
}