/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 */
package org.biojava.nbio.structure.align.gui.jmol;

import java.awt.Color;
import java.awt.Container;
import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.io.StringWriter;
import java.util.ArrayList;
import java.util.List;

import javax.swing.Box;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JMenuBar;
import javax.swing.JTextField;

import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.PDBHeader;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.StructureIdentifier;
import org.biojava.nbio.structure.align.gui.MenuCreator;
import org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI;
import org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay;
import org.biojava.nbio.structure.align.multiple.Block;
import org.biojava.nbio.structure.align.multiple.BlockSet;
import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools;
import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter;
import org.biojava.nbio.structure.align.webstart.AligUIManager;
import org.biojava.nbio.structure.jama.Matrix;
import org.forester.archaeopteryx.Archaeopteryx;
import org.forester.phylogeny.Phylogeny;
import org.jcolorbrewer.ColorBrewer;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
 * A class that provides a 3D visualization Frame in Jmol for
 * {@link MultipleAlignment}s.
 *
 * @author Aleix Lafita
 * @since 4.1.0
 *
 */
public class MultipleAlignmentJmol extends AbstractAlignmentJmol {

	private MultipleAlignment multAln;
	private List<Atom[]> transformedAtoms;
	private JCheckBox colorByBlocks;
	private List<JCheckBox> selectedStructures;

	private static final String LIGAND_DISPLAY_SCRIPT = "select ligand; wireframe 40; spacefill 120; color CPK;";

	private static final Logger logger = LoggerFactory
			.getLogger(MultipleAlignmentJmol.class);

	/**
	 * Default constructor creates an empty JmolPanel window, from where
	 * alignments can be made through the align menu.
	 */
	public MultipleAlignmentJmol() {
		this(null, null);
	}

	/**
	 * The constructor displays the Mutltiple Alignment in a new JmolPanel
	 * Frame.
	 *
	 * @param msa
	 *            : contains the aligned residues.
	 * @param rotatedAtoms
	 *            : contains the transformed Atom coordinates.
	 */
	public MultipleAlignmentJmol(MultipleAlignment msa,
			List<Atom[]> rotatedAtoms) {

		AligUIManager.setLookAndFeel();
		nrOpenWindows++;
		jmolPanel = new JmolPanel();
		frame = new JFrame();
		JMenuBar menu = MenuCreator.initJmolMenu(frame, this, null, msa);

		frame.setJMenuBar(menu);
		this.multAln = msa;
		this.transformedAtoms = rotatedAtoms;
		this.selectedStructures = new ArrayList<JCheckBox>();

		frame.addWindowListener(new WindowAdapter() {

			@Override
			public void windowClosing(WindowEvent e) {

				nrOpenWindows--;
				destroy();

				if (nrOpenWindows > 0)
					frame.dispose();
				else {
					MultipleAlignmentGUI gui = MultipleAlignmentGUI
							.getInstanceNoVisibilityChange();
					if (gui.isVisible()) {
						frame.dispose();
						gui.requestFocus();
					} else
						System.exit(0);
				}
			}
		});

		Container contentPane = frame.getContentPane();
		Box vBox = Box.createVerticalBox();

		jmolPanel.addMouseMotionListener(this);
		jmolPanel.addMouseListener(this);
		jmolPanel
				.setPreferredSize(new Dimension(DEFAULT_WIDTH, DEFAULT_HEIGHT));

		vBox.add(jmolPanel);

		// / USER SCRIPTING COMMAND
		JTextField field = new JTextField();

		field.setMaximumSize(new Dimension(Short.MAX_VALUE, 30));
		field.setText(COMMAND_LINE_HELP);
		RasmolCommandListener listener = new RasmolCommandListener(jmolPanel,
				field);

		field.addActionListener(listener);
		field.addMouseListener(listener);
		field.addKeyListener(listener);
		vBox.add(field);

		// / STRUCTURE SELECTION
		if (multAln != null) {

			Box hBox00 = Box.createHorizontalBox();
			hBox00.setMaximumSize(new Dimension(Short.MAX_VALUE, 30));
			
			JButton show = new JButton("Show Only: ");
			show.addActionListener(new ActionListener() {

				@Override
				public void actionPerformed(ActionEvent e) {
					jmolPanel.evalString("save selection;");
					String cmd = getJmolString(multAln,
							transformedAtoms, colorPalette,
							colorByBlocks.isSelected());
					cmd += "; restrict ";
					for (int st = 0; st < multAln.size(); st++) {
						if (selectedStructures.get(st).isSelected()) {
							cmd += "*/" + (st + 1) + ", ";
						}
					}
					cmd += "none;";
					jmolPanel.executeCmd(cmd + " restore selection;");
				}
			});
			hBox00.add(show);
			hBox00.add(Box.createGlue());
			vBox.add(hBox00);
		
			// A line of structures of maximum 5
			for (int line = 0; line < 1 + (multAln.size() / 5); line++) {
				Box hBox0 = Box.createHorizontalBox();
				hBox0.setMaximumSize(new Dimension(Short.MAX_VALUE, 30));

				for (int str = line * 5; str < Math.min((line + 1) * 5,
						multAln.size()); str++) {
					JCheckBox structureSelection = new JCheckBox(multAln
							.getEnsemble().getStructureIdentifiers().get(str)
							.getIdentifier());
					hBox0.add(structureSelection);
					hBox0.add(Box.createGlue());
					structureSelection.setSelected(true);
					selectedStructures.add(structureSelection);
				}

				vBox.add(hBox0);
			}
		}

		// / COMBO BOXES
		Box hBox1 = Box.createHorizontalBox();
		hBox1.add(Box.createGlue());

		String[] styles = new String[] { "Cartoon", "Backbone", "CPK",
				"Ball and Stick", "Ligands", "Ligands and Pocket" };
		JComboBox style = new JComboBox(styles);

		hBox1.setMaximumSize(new Dimension(Short.MAX_VALUE, 30));

		hBox1.add(new JLabel("Style"));
		hBox1.add(style);
		vBox.add(hBox1);
		contentPane.add(vBox);

		style.addActionListener(jmolPanel);

		String[] colorModes = new String[] { "Secondary Structure", "By Chain",
				"Rainbow", "By Element", "By Amino Acid", "Hydrophobicity",
				"Suggest Domains", "Show SCOP Domains" };
		JComboBox jcolors = new JComboBox(colorModes);
		jcolors.addActionListener(jmolPanel);

		hBox1.add(Box.createGlue());
		hBox1.add(new JLabel("Color"));
		hBox1.add(jcolors);

		String[] cPalette = { "Spectral", "Set1", "Set2", "Pastel" };
		JComboBox palette = new JComboBox(cPalette);

		palette.addActionListener(new ActionListener() {
			@Override
			public void actionPerformed(ActionEvent e) {

				JComboBox source = (JComboBox) e.getSource();
				String value = source.getSelectedItem().toString();
				evalString("save selection; select *; color grey; "
						+ "select ligand; color CPK;");

				if (value == "Set1") {
					colorPalette = ColorBrewer.Set1;
				} else if (value == "Set2") {
					colorPalette = ColorBrewer.Set2;
				} else if (value == "Spectral") {
					colorPalette = ColorBrewer.Spectral;
				} else if (value == "Pastel") {
					colorPalette = ColorBrewer.Pastel1;
				}
				String script = getJmolString(multAln, transformedAtoms,
						colorPalette, colorByBlocks.isSelected());
				evalString(script + "; restore selection; ");
			}
		});

		hBox1.add(Box.createGlue());
		hBox1.add(new JLabel("Palette"));
		hBox1.add(palette);

		// / CHECK BOXES
		Box hBox2 = Box.createHorizontalBox();

		JButton resetDisplay = new JButton("Reset Display");
		resetDisplay.addActionListener(new ActionListener() {

			@Override
			public void actionPerformed(ActionEvent e) {
				logger.info("reset!!");
				jmolPanel.executeCmd("restore STATE state_1");

			}
		});

		hBox2.add(resetDisplay);
		hBox2.add(Box.createGlue());

		JCheckBox toggleSelection = new JCheckBox("Show Selection");
		toggleSelection.addItemListener(new ItemListener() {

			@Override
			public void itemStateChanged(ItemEvent e) {
				boolean showSelection = (e.getStateChange() == ItemEvent.SELECTED);

				if (showSelection) {
					jmolPanel.executeCmd("set display selected");
				} else
					jmolPanel.executeCmd("set display off");
			}
		});
		hBox2.add(toggleSelection);
		hBox2.add(Box.createGlue());

		colorByBlocks = new JCheckBox("Color By Block");
		colorByBlocks.addItemListener(new ItemListener() {
			@Override
			public void itemStateChanged(ItemEvent e) {
				evalString("save selection; "
						+ getJmolString(multAln, transformedAtoms,
								colorPalette, colorByBlocks.isSelected())
						+ "; restore selection;");
			}
		});

		hBox2.add(colorByBlocks);
		hBox2.add(Box.createGlue());

		vBox.add(hBox2);

		// STATUS DISPLAY
		Box hBox = Box.createHorizontalBox();

		status = new JTextField();
		status.setBackground(Color.white);
		status.setEditable(false);
		status.setMaximumSize(new Dimension(Short.MAX_VALUE, 30));
		status.setPreferredSize(new Dimension(DEFAULT_WIDTH / 2, 30));
		status.setMinimumSize(new Dimension(DEFAULT_WIDTH / 2, 30));
		hBox.add(status);

		text = new JTextField();
		text.setBackground(Color.white);
		text.setMaximumSize(new Dimension(Short.MAX_VALUE, 30));
		text.setPreferredSize(new Dimension(DEFAULT_WIDTH / 2, 30));
		text.setMinimumSize(new Dimension(DEFAULT_WIDTH / 2, 30));
		text.setText("Display of Atom info");
		text.setEditable(false);
		hBox.add(text);

		vBox.add(hBox);

		contentPane.add(vBox);
		MyJmolStatusListener li = (MyJmolStatusListener) jmolPanel
				.getStatusListener();

		li.setTextField(status);
		frame.pack();
		frame.setVisible(true);

		initCoords();
		resetDisplay();
	}

	@Override
	protected void initCoords() {
		try {
			if (multAln == null) {
				if (structure != null)
					setStructure(structure);
				else {
					logger.error("Could not find anything to display!");
					return;
				}
			}
			PDBHeader header = new PDBHeader();
			String title = multAln.getEnsemble().getAlgorithmName() + " V."
					+ multAln.getEnsemble().getVersion() + " : ";

			for (StructureIdentifier name : multAln.getEnsemble()
					.getStructureIdentifiers()) {
				title += name.getIdentifier() + " ";
			}
			Structure artificial = MultipleAlignmentJmolDisplay
					.getAlignedStructure(transformedAtoms);

			artificial.setPDBHeader(header);
			setStructure(artificial);
			header.setTitle(title);
			logger.info(title);

		} catch (StructureException e) {
			e.printStackTrace();
		}
	}

	@Override
	public void destroy() {
		super.destroy();
		multAln = null;
		transformedAtoms = null;
	}

	@Override
	public void actionPerformed(ActionEvent ae) {
		String cmd = ae.getActionCommand();
		if (multAln == null) {
			logger.error("Currently not viewing an alignment!");
			return;
		}
		try {
			if (cmd.equals(MenuCreator.TEXT_ONLY)) {
				logger.warn("Option not available for MultipleAlignments");

			} else if (cmd.equals(MenuCreator.PAIRS_ONLY)) {
				String result = MultipleAlignmentWriter
						.toAlignedResidues(multAln);
				MultipleAlignmentJmolDisplay
						.showAlignmentImage(multAln, result);

			} else if (cmd.equals(MenuCreator.ALIGNMENT_PANEL)) {
				MultipleAlignmentJmolDisplay.showMultipleAligmentPanel(multAln,
						this);

			} else if (cmd.equals(MenuCreator.FATCAT_TEXT)) {
				String result = MultipleAlignmentWriter.toFatCat(multAln)
						+ "\n";
				result += MultipleAlignmentWriter.toTransformMatrices(multAln);
				MultipleAlignmentJmolDisplay
						.showAlignmentImage(multAln, result);

			} else if (cmd.equals(MenuCreator.PHYLOGENETIC_TREE)) {

				// Kimura, Structural and Fractional Dissimilarity Score
				Phylogeny kimura = MultipleAlignmentTools
						.getKimuraTree(multAln);
				Phylogeny sdm = MultipleAlignmentTools.getHSDMTree(multAln);
				// Phylogeny structural = MultipleAlignmentTools
				// .getStructuralTree(multAln);

				Archaeopteryx
						.createApplication(new Phylogeny[] { kimura, sdm });
			}
		} catch (Exception e) {
			logger.error("Could not complete display option.", e);
		}
	}

	/**
	 * Generate a Jmol command String that colors the aligned residues of every
	 * structure.
	 */
	public static String getJmolString(MultipleAlignment multAln,
			List<Atom[]> transformedAtoms, ColorBrewer colorPalette,
			boolean colorByBlocks) {

		// Color by blocks if specified
		if (colorByBlocks)
			return getMultiBlockJmolString(multAln, transformedAtoms,
					colorPalette, colorByBlocks);
		Color[] colors = colorPalette.getColorPalette(multAln.size());

		StringBuffer j = new StringBuffer();
		j.append(DEFAULT_SCRIPT);

		// Color the equivalent residues of every structure
		StringBuffer sel = new StringBuffer();
		sel.append("select *; color lightgrey; backbone 0.1; ");
		List<List<String>> allPDB = new ArrayList<List<String>>();

		// Get the aligned residues of every structure
		for (int i = 0; i < multAln.size(); i++) {

			List<String> pdb = MultipleAlignmentJmolDisplay.getPDBresnum(i,
					multAln, transformedAtoms.get(i));

			allPDB.add(pdb);
			sel.append("select ");
			int pos = 0;
			for (String res : pdb) {
				if (pos > 0)
					sel.append(",");
				pos++;

				sel.append(res);
				sel.append("/" + (i + 1));
			}
			if (pos == 0)
				sel.append("none");
			sel.append("; backbone 0.3 ; color [" + colors[i].getRed() + ","
					+ colors[i].getGreen() + "," + colors[i].getBlue() + "]; ");
		}

		j.append(sel);
		j.append("model 0;  ");
		j.append(LIGAND_DISPLAY_SCRIPT);

		return j.toString();
	}

	/**
	 * Colors every Block of the structures with a different color, following
	 * the palette. It colors each Block differently, no matter if it is from
	 * the same or different BlockSet.
	 */
	public static String getMultiBlockJmolString(MultipleAlignment multAln,
			List<Atom[]> transformedAtoms, ColorBrewer colorPalette,
			boolean colorByBlocks) {

		StringWriter jmol = new StringWriter();
		jmol.append(DEFAULT_SCRIPT);
		jmol.append("select *; color lightgrey; backbone 0.1; ");

		int blockNum = multAln.getBlocks().size();
		Color[] colors = colorPalette.getColorPalette(blockNum);

		// For every structure color all the blocks with the printBlock method
		for (int str = 0; str < transformedAtoms.size(); str++) {
			jmol.append("select */" + (str + 1) + "; color lightgrey; model "
					+ (str + 1) + "; ");

			int index = 0;
			for (BlockSet bs : multAln.getBlockSets()) {
				for (Block b : bs.getBlocks()) {

					List<List<Integer>> alignRes = b.getAlignRes();
					printJmolScript4Block(transformedAtoms.get(str), alignRes,
							colors[index], jmol, str, index, blockNum);
					index++;
				}
			}
		}

		jmol.append("model 0;  ");
		jmol.append(LIGAND_DISPLAY_SCRIPT);

		return jmol.toString();
	}

	private static void printJmolScript4Block(Atom[] atoms,
			List<List<Integer>> alignRes, Color blockColor, StringWriter jmol,
			int str, int colorPos, int blockNum) {

		// Obtain the residues aligned in this block of the structure
		List<String> pdb = new ArrayList<String>();
		for (int i = 0; i < alignRes.get(str).size(); i++) {

			// Handle gaps - only color if it is not null
			if (alignRes.get(str).get(i) != null) {
				int pos = alignRes.get(str).get(i);
				pdb.add(JmolTools.getPdbInfo(atoms[pos]));
			}
		}

		// Select the aligned residues
		StringBuffer buf = new StringBuffer("select ");
		int count = 0;
		for (String res : pdb) {
			if (count > 0)
				buf.append(",");
			buf.append(res);
			buf.append("/" + (str + 1));
			count++;
		}

		buf.append("; backbone 0.3 ; color [" + blockColor.getRed() + ","
				+ blockColor.getGreen() + "," + blockColor.getBlue() + "]; ");

		jmol.append(buf);
	}

	@Override
	public void resetDisplay() {

		if (multAln != null && transformedAtoms != null) {
			String script = getJmolString(multAln, transformedAtoms,
					colorPalette, colorByBlocks.isSelected());
			logger.debug(script);
			evalString(script);
			jmolPanel.evalString("save STATE state_1");
		}
	}

	@Override
	public List<Matrix> getDistanceMatrices() {
		if (multAln == null)
			return null;
		else
			return multAln.getEnsemble().getDistanceMatrix();
	}

	public void setColorByBlocks(boolean colorByBlocks) {
		this.colorByBlocks.setSelected(colorByBlocks);
		resetDisplay();
	}

	public JFrame getFrame() {
		return frame;
	}

	public MultipleAlignment getMultipleAlignment() {
		return multAln;
	}

}
