ControlPanel.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.controlPanel;

import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.Insets;
import java.util.List;

import javax.swing.JButton;
import javax.swing.JPanel;

import edu.yu.einstein.genplay.core.manager.project.ProjectChromosomes;
import edu.yu.einstein.genplay.core.manager.project.ProjectManager;
import edu.yu.einstein.genplay.core.manager.project.ProjectWindow;
import edu.yu.einstein.genplay.dataStructure.genomeWindow.SimpleGenomeWindow;



/**
 * A ControlPanel component
 * @author Julien Lajugie
 * @author Nicolas Fourel
 * @version 0.1
 */
public final class ControlPanel extends JPanel {

	private static final long serialVersionUID = -8254420324898563978L; // generated ID
	private static final int INCREMENT_FACTOR = 10; 					// the length of a left or right move is the length of the
	// displayed chromosome window divided by this constant
	private final TopPanel							topPanel;			// TopPanel part (multi genome button and position scroll bar)
	private final ZoomPanel 						zoomPanel;			// ZoomPanel part
	private final ChromosomePanel 					chromosomePanel;	// ChromosomePanel part
	private final GenomeWindowPanel 				genomeWindowPanel;	// GenomeWindowPanel part
	private final ProjectWindow						projectWindow;		// Instance of the Genome Window Manager


	/**
	 * Creates an instance of {@link ControlPanel}
	 */
	public ControlPanel() {
		topPanel = new TopPanel();
		zoomPanel = new ZoomPanel();
		chromosomePanel = new ChromosomePanel();
		genomeWindowPanel = new GenomeWindowPanel();

		projectWindow = ProjectManager.getInstance().getProjectWindow();

		// Add the components
		setLayout(new GridBagLayout());
		GridBagConstraints gbc = new GridBagConstraints();

		gbc.fill = GridBagConstraints.BOTH;
		gbc.insets = new Insets(0, 0, 10, 0);
		gbc.gridx = 0;
		gbc.gridy = 0;
		gbc.weightx = 1;
		gbc.weighty = 1;
		gbc.gridwidth = 3;
		add(topPanel, gbc);

		gbc.fill = GridBagConstraints.NONE;
		gbc.anchor = GridBagConstraints.LAST_LINE_START;
		gbc.insets = new Insets(0, 10, 0, 0);
		gbc.gridx = 0;
		gbc.gridy = 1;
		gbc.weightx = 1;
		gbc.gridwidth = 1;
		add(zoomPanel, gbc);

		gbc.anchor = GridBagConstraints.PAGE_END;
		gbc.insets = new Insets(0, 10, 0, 10);
		gbc.gridx = 1;
		gbc.weightx = 0;
		add(chromosomePanel, gbc);

		gbc.anchor = GridBagConstraints.LAST_LINE_END;
		gbc.insets = new Insets(0, 0, 0, 10);
		gbc.gridx = 2;
		gbc.weightx = 1;
		add(genomeWindowPanel, gbc);

		// register the control panel to the project window manager so the control panel can be notified when the project window changes
		registerToGenomeWindow();

		setOpaque(false);
	}


	/**
	 * @return the button to jump on a genomic position
	 */
	public JButton getJumpButton() {
		return genomeWindowPanel.getJumpButton();
	}


	/**
	 * Decrements the start and the stop positions of the {@link SimpleGenomeWindow}.
	 * The move is 4/5 of the width of the tracks panel.
	 */
	public void moveFarLeft() {
		int moveGap = (int) (projectWindow.getGenomeWindow().getSize() / (double) INCREMENT_FACTOR);
		moveGap *= 5;
		moveGapLeft(moveGap);
	}


	/**
	 * Increments the start and the stop positions of the {@link SimpleGenomeWindow}.
	 * The move is 4/5 of the width of the tracks panel.
	 */
	public void moveFarRight() {
		int moveGap = (int) (projectWindow.getGenomeWindow().getSize() / (double) INCREMENT_FACTOR);
		moveGap *= 5;
		moveGapRight(moveGap);
	}


	/**
	 * Decrements the start and the stop positions of the {@link SimpleGenomeWindow}.
	 * @param moveGap the gap to use
	 */
	private void moveGapLeft(int moveGap) {
		// we want to move from at least 1 nucleotide
		moveGap = Math.max(moveGap, 1);
		SimpleGenomeWindow newGenomeWindow = new SimpleGenomeWindow(projectWindow.getGenomeWindow().getChromosome(), projectWindow.getGenomeWindow().getStart() - moveGap, projectWindow.getGenomeWindow().getStop() - moveGap);
		if (newGenomeWindow.getMiddlePosition() < 0) {
			int size = newGenomeWindow.getSize();
			int start = -size / 2;
			int stop = newGenomeWindow.getStart() + size;
			newGenomeWindow = new SimpleGenomeWindow(newGenomeWindow.getChromosome(), start, stop);
		}
		projectWindow.setGenomeWindow(newGenomeWindow);
	}


	/**
	 * Increments the start and the stop positions of the {@link SimpleGenomeWindow}.
	 * @param moveGap the gap to use
	 */
	private void moveGapRight(int moveGap) {
		// we want to move from at least 1 nucleotide
		moveGap = Math.max(moveGap, 1);
		SimpleGenomeWindow newGenomeWindow = new SimpleGenomeWindow(projectWindow.getGenomeWindow().getChromosome(), projectWindow.getGenomeWindow().getStart() + moveGap, projectWindow.getGenomeWindow().getStop() + moveGap);
		if (newGenomeWindow.getMiddlePosition() > projectWindow.getGenomeWindow().getChromosome().getLength()) {
			int size = newGenomeWindow.getSize();
			int start = projectWindow.getGenomeWindow().getChromosome().getLength() - (size / 2);
			int stop = newGenomeWindow.getStart() + size;
			newGenomeWindow = new SimpleGenomeWindow(newGenomeWindow.getChromosome(), start, stop);
		}
		projectWindow.setGenomeWindow(newGenomeWindow);
	}


	/**
	 * Decrements the start and the stop positions of the {@link SimpleGenomeWindow}.
	 * The move is 1/10 of the width of the tracks panel.
	 */
	public void moveLeft() {
		int moveGap = (int) (projectWindow.getGenomeWindow().getSize() / (double) INCREMENT_FACTOR);
		moveGapLeft(moveGap);
	}


	/**
	 * Increments the start and the stop positions of the {@link SimpleGenomeWindow}.
	 * The move is 1/10 of the width of the tracks panel.
	 */
	public void moveRight() {
		int moveGap = (int) (projectWindow.getGenomeWindow().getSize() / (double) INCREMENT_FACTOR);
		moveGapRight(moveGap);
	}


	/**
	 * Registers every control panel components to the genome window manager.
	 */
	private void registerToGenomeWindow () {
		projectWindow.addGenomeWindowListener(chromosomePanel);
		projectWindow.addGenomeWindowListener(genomeWindowPanel);
		projectWindow.addGenomeWindowListener(topPanel);
		projectWindow.addGenomeWindowListener(zoomPanel);
	}


	/**
	 * This method reinitializes the elements of the
	 * chromosome panel with the values of the {@link ProjectChromosomes}.
	 * This method needs to be called when the chomosome manager changes.
	 */
	public void reinitChromosomePanel () {
		chromosomePanel.updateChromosomePanel();
	}


	/**
	 * @param genomeNames genome names to replace to the genome selector (multi genome only)
	 */
	public void resetGenomeNames (List<String> genomeNames) {
		genomeWindowPanel.resetGenomeNames(genomeNames);
	}


	/**
	 * Enables or disables the control panel
	 * @param b a boolean value, where true enables the component and false disables it
	 */
	@Override
	public void setEnabled(boolean b) {
		chromosomePanel.setEnaled(b);
		genomeWindowPanel.setEnaled(b);
		topPanel.setEnabled(b);
		super.setEnabled(b);
	}


	/**
	 * @param genomeName genome name to select in the genome selector (multi genome only)
	 */
	public void setSelectedGenomeName (String genomeName) {
		genomeWindowPanel.setSelectedGenomeName(genomeName);
	}


	/**
	 * Zooms in
	 */
	public void zoomIn() {
		int newZoom = ProjectManager.getInstance().getProjectZoom().getNextZoomIn(projectWindow.getGenomeWindow().getSize());
		zoomPanel.zoomChanged(newZoom);
	}


	/**
	 * Zooms out
	 */
	public void zoomOut() {
		int newZoom = ProjectManager.getInstance().getProjectZoom().getNextZoomOut(projectWindow.getGenomeWindow().getSize());
		zoomPanel.zoomChanged(newZoom);
	}
}