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/*
 *                    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;

import java.awt.Dimension;
import java.util.ArrayList;
import java.util.List;

import javax.swing.Box;
import javax.swing.JFrame;
import javax.swing.JMenuBar;
import javax.swing.JScrollPane;

import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel;
import org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay;
import org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol;
import org.biojava.nbio.structure.align.gui.jmol.JmolTools;
import org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol;
import org.biojava.nbio.structure.align.multiple.Block;
import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentDisplay;
//import org.slf4j.Logger;
//import org.slf4j.LoggerFactory;

/**
 * Utility Class that provides helper methods for the visualization of
 * {@link MultipleAlignment}s.
 * 
 * Currently supported: Alignment Panel Display, select aligned
 * residues in Jmol by their PDB name, show a text Frame for any sequence
 * alignment format, basic Jmol display from a MultipleAlignment, generate
 * an artificial PDB structure with a new model for every aligned structure.
 *
 * @author Aleix Lafita
 * @since 4.2.0
 *
 */
public class MultipleAlignmentJmolDisplay  {

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

	/**
	 * Utility method used in the {@link MultipleAlignmentJmol} Frame,
	 * when the aligned residues of a structure in the alignment have
	 * to be selected for formatting them (coloring and style).
	 *
	 * @param structNum the structure index (row) of the alignment
	 * @param multAln the MultipleAlignment that contains the equivalent
	 * 			positions
	 * @param ca the atom array of the structure specified
	 * 			(corresponding to the structure index)
	 * @return List of pdb Strings corresponding to the aligned positions
	 * 			of the structure.
	 */
	public static List getPDBresnum(int structNum,
			MultipleAlignment multAln, Atom[] ca){

		List lst = new ArrayList();

		for(Block block : multAln.getBlocks() ) {

			for (int i=0; i rotatedAtoms = MultipleAlignmentDisplay.getRotatedAtoms(multAln);

		MultipleAlignmentJmol jmol =
				new MultipleAlignmentJmol(multAln, rotatedAtoms);

		jmol.setTitle(jmol.getStructure().getPDBHeader().getTitle());
		return jmol;
	}

}