BinListScaler.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.gui.dataScalerForTrackDisplay;

import edu.yu.einstein.genplay.core.manager.project.ProjectManager;
import edu.yu.einstein.genplay.dataStructure.chromosome.Chromosome;
import edu.yu.einstein.genplay.dataStructure.genomeWindow.GenomeWindow;
import edu.yu.einstein.genplay.dataStructure.list.chromosomeWideList.SCWListView.bin.BinListViewBuilder;
import edu.yu.einstein.genplay.dataStructure.list.genomeWideList.SCWList.binList.BinList;
import edu.yu.einstein.genplay.dataStructure.list.listView.ListView;
import edu.yu.einstein.genplay.dataStructure.scoredChromosomeWindow.ScoredChromosomeWindow;
import edu.yu.einstein.genplay.exception.ExceptionManager;
import edu.yu.einstein.genplay.exception.exceptions.InvalidChromosomeException;
import edu.yu.einstein.genplay.util.ListView.ChromosomeWindowListViews;


/**
 * This class scales a {@link BinList} to be displayed on a track.
 * @author Julien Lajugie
 */
class BinListScaler implements DataScalerForTrackDisplay<BinList, ListView<ScoredChromosomeWindow>> {

	/**
	 * Threads that computes the scaled data for the chromosome currently displayed
	 * at the current zoom level and screen resolution.
	 * @author Julien Lajugie
	 */
	private class ScalerThread extends Thread {

		@Override
		public void run() {
			Thread thisThread = Thread.currentThread();
			setName("Data Scaler Thread");
			ListView<ScoredChromosomeWindow> currentChromosomeList;
			try {
				currentChromosomeList = dataToScale.get(scaledChromosome);
			} catch (InvalidChromosomeException e) {
				ExceptionManager.getInstance().caughtException(e);
				return;
			}
			if ((currentChromosomeList == null) || currentChromosomeList.isEmpty()) {
				scaledSCWList = currentChromosomeList;
				return;
			}
			int binSize = dataToScale.getBinSize();
			if ((scaledXRatio * binSize) >= 1) {
				scaledSCWList = currentChromosomeList;
				DataScalerManager.getInstance().redrawLayers(BinListScaler.this);
				return;
			}
			int chromosomeIndex = ProjectManager.getInstance().getProjectChromosomes().getIndex(scaledChromosome);
			int i = 0;
			double ratio = scaledXRatio * dataToScale.getBinSize() * BinList.AVERAGE_BIN_SIZE_FACTORS[i];
			while ((i < BinList.AVERAGE_BIN_SIZE_FACTORS.length) && (ratio < 1)) {
				if (thisThread != scalerThread) {
					return;
				}
				currentChromosomeList = dataToScale.getAveragedList(i).get(chromosomeIndex);
				binSize = dataToScale.getBinSize() * BinList.AVERAGE_BIN_SIZE_FACTORS[i];
				i++;
				if (i < BinList.AVERAGE_BIN_SIZE_FACTORS.length) {
					ratio = scaledXRatio * dataToScale.getBinSize() * BinList.AVERAGE_BIN_SIZE_FACTORS[i];
				}
			}
			if ((scaledXRatio * binSize) >= 1) {
				scaledSCWList = currentChromosomeList;
				DataScalerManager.getInstance().redrawLayers(BinListScaler.this);
				return;
			}

			// we calculate how many windows are printable depending on the screen resolution
			int binSizeRatio  = (int) (1 / (binSize * scaledXRatio));
			int fittedBinSize = binSizeRatio * binSize;

			// if the fitted bin size is smaller than the regular bin size we don't modify the data
			if (fittedBinSize <= binSize) {
				scaledSCWList = currentChromosomeList;
				DataScalerManager.getInstance().redrawLayers(BinListScaler.this);
				return;
			}
			// create a list adapted to the xRatio
			BinListViewBuilder blvb = new BinListViewBuilder(fittedBinSize);
			for(int index = 0; index < currentChromosomeList.size(); index += binSizeRatio) {
				if (thisThread != scalerThread) {
					return;
				}
				float sum = 0;
				int n = 0;
				for(int j = 0; (j < binSizeRatio) && (thisThread == scalerThread); j ++) {
					if (((index + j) < currentChromosomeList.size()) && (currentChromosomeList.get(index + j).getScore() != 0)) {
						sum += currentChromosomeList.get(index + j).getScore();
						n++;
					}
				}
				if (n > 0) {
					blvb.addElementToBuild(sum / n);
				}
				else {
					blvb.addElementToBuild(0);
				}
			}
			scaledSCWList = blvb.getListView();
			DataScalerManager.getInstance().redrawLayers(BinListScaler.this);
		}
	}


	/** Thread that scales the data */
	private ScalerThread scalerThread;

	/** Scaled chromosome */
	private Chromosome scaledChromosome;

	/** Scaled xRatio (ratio between the track width and the displayed genome window width) */
	private double scaledXRatio;

	/** The scw list scaled for a specified chromosome and xRatio */
	private ListView<ScoredChromosomeWindow> scaledSCWList;

	/** Data to be scaled for track display */
	private final BinList dataToScale;


	/**
	 * Creates an instance of {@link BinListScaler}
	 * @param dataToScale the data that needs to be scaled
	 */
	BinListScaler(BinList dataToScale) {
		this.dataToScale = dataToScale;
	}


	@Override
	public ListView<ScoredChromosomeWindow> getDataScaledForTrackDisplay() {
		GenomeWindow projectWindow = ProjectManager.getInstance().getProjectWindow().getGenomeWindow();
		double projectXRatio = ProjectManager.getInstance().getProjectWindow().getXRatio();
		// if the chromosome or the xRatio of the project window changed we need to rescale the data
		if (!projectWindow.getChromosome().equals(scaledChromosome) || (projectXRatio != scaledXRatio)) {
			scaledChromosome = projectWindow.getChromosome();
			scaledXRatio = projectXRatio;
			scaleChromosome();
		}
		if (scaledSCWList == null) {
			return null;
		}
		return ChromosomeWindowListViews.subList(scaledSCWList, projectWindow.getStart(), projectWindow.getStop());
	}


	@Override
	public BinList getDataToScale() {
		return dataToScale;
	}


	/**
	 * Starts the thread that scales the current chromosome
	 * for the current zoom level and screen resolution
	 */
	private void scaleChromosome() {
		scaledSCWList = null;
		scalerThread = new ScalerThread();
		scalerThread.start();
	}
}