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The protein structure modules of BioJava.
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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.multiple;

import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import java.util.Locale;

import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.StructureIdentifier;

/**
 * A general implementation of a {@link MultipleAlignment}.
 *
 * @author Aleix Lafita
 * @since 4.1.0
 *
 */
public class MultipleAlignmentImpl extends AbstractScoresCache implements
		Serializable, MultipleAlignment, Cloneable {

	private static final long serialVersionUID = 3432043794125805139L;

	private MultipleAlignmentEnsemble parent;
	private List blockSets;

	// Cache variables (can be updated)
	private int length;
	private int coreLength;
	private List alignResCounts;
	private List coverages;

	/**
	 * Default Constructor. Empty alignment. No structures assigned.
	 *
	 * @return MultipleAlignment an empty MultipleAlignment instance.
	 */
	public MultipleAlignmentImpl() {
		this(new MultipleAlignmentEnsembleImpl()); // assign an empty ensemble.
	}

	/**
	 * Constructor linking to an existing ensemble. Automatically adds this
	 * alignment to the parent ensemble.
	 *
	 * @param ensemble
	 *            parent MultipleAlignmentEnsemble.
	 * @return MultipleAlignment an alignment instance part of an ensemble.
	 */
	public MultipleAlignmentImpl(MultipleAlignmentEnsemble ensemble) {

		super();
		parent = ensemble;
		if (parent != null)
			parent.getMultipleAlignments().add(this);

		blockSets = null;

		length = -1; // Value -1 reserved to indicate that has to be calculated
		coreLength = -1;
		alignResCounts = null; // Value null means not set
		coverages = null;
	}

	/**
	 * Copy constructor. Recursively copies member BlockSets.
	 *
	 * @param ma
	 *            MultipleAlignmentImpl to copy.
	 * @return MultipleAlignmentImpl identical copy of the alignment.
	 */
	public MultipleAlignmentImpl(MultipleAlignmentImpl ma) {

		super(ma); // Copy the scores
		parent = ma.parent;

		length = ma.length;
		coreLength = ma.coreLength;

		blockSets = null;
		if (ma.blockSets != null) {
			// Make a deep copy of everything
			this.blockSets = new ArrayList<>();
			for (BlockSet bs : ma.blockSets) {
				BlockSet newBS = bs.clone();
				newBS.setMultipleAlignment(this);
				this.blockSets.add(newBS);
			}
		}
	}

	@Override
	public void clear() {
		super.clear();
		length = -1;
		coreLength = -1;
		alignResCounts = null;
		for (BlockSet a : getBlockSets()) {
			a.clear();
		}
	}

	@Override
	public MultipleAlignmentImpl clone() {
		return new MultipleAlignmentImpl(this);
	}

	@Override
	public String toString() {
		List ids = new ArrayList<>(parent
				.getStructureIdentifiers().size());
		for (StructureIdentifier i : parent.getStructureIdentifiers()) {
			ids.add(i.getIdentifier());
		}
		String resume = "Structures:" + ids + " \nAlgorithm:"
				+ parent.getAlgorithmName() + "_" + parent.getVersion()
				+ " \nBlockSets: " + getBlockSets().size() + " \nBlocks: "
				+ getBlocks().size() + " \nLength: " + length()
				+ " \nCore Length: " + getCoreLength();
		for (String score : getScores()) {
			resume += " \n" + score + ": ";
			resume += String.format(Locale.US, "%.2f", getScore(score));
		}
		return resume;
	}

	@Override
	public List getBlockSets() {
		if (blockSets == null)
			blockSets = new ArrayList<>();
		return blockSets;
	}

	@Override
	public List getBlocks() {
		List blocks = new ArrayList<>();
		for (BlockSet bs : getBlockSets()) {
			blocks.addAll(bs.getBlocks());
		}
		return blocks;
	}

	@Override
	public void setBlockSets(List blockSets) {
		this.blockSets = blockSets;
	}

	@Override
	public BlockSet getBlockSet(int index) {
		return blockSets.get(index);
	}

	@Override
	public Block getBlock(int index) {
		List blocks = getBlocks();
		return blocks.get(index);
	}

	@Override
	public List getAtomArrays() {
		return parent.getAtomArrays();
	}

	@Override
	public StructureIdentifier getStructureIdentifier(int index) {
		return parent.getStructureIdentifiers().get(index);
	}

	@Override
	public int size() {
		return parent.size();
	}

	@Override
	public int length() {
		if (length < 0)
			updateLength();
		return length;
	}

	@Override
	public int getCoreLength() {
		if (coreLength < 0)
			updateCoreLength();
		return coreLength;
	}

	/**
	 * Force recalculation of the length (aligned columns) based on the BlockSet
	 * lengths.
	 */
	protected void updateLength() {
		if (getBlockSets().size() == 0) {
			throw new IndexOutOfBoundsException(
					"Empty MultipleAlignment: blockSets size == 0.");
		} // Otherwise try to calculate it from the BlockSet information
		else {
			length = 0;
			for (BlockSet blockSet : blockSets)
				length += blockSet.length();
		}
	}

	/**
	 * Force recalculation of the core length (ungapped columns) based on the
	 * BlockSet core lengths.
	 */
	protected void updateCoreLength() {
		if (getBlockSets().size() == 0) {
			throw new IndexOutOfBoundsException(
					"Empty MultipleAlignment: blockSets size == 0.");
		} // Otherwise try to calculate it from the BlockSet information
		else {
			coreLength = 0;
			for (BlockSet blockSet : blockSets)
				coreLength += blockSet.getCoreLength();
		}
	}

	/**
	 * Updates all cached properties
	 *
	 * @throws StructureException
	 */
	protected void updateCache() {
		updateCoreLength();
		updateLength();
	}

	@Override
	public MultipleAlignmentEnsemble getEnsemble() {
		return parent;
	}

	@Override
	public void setEnsemble(MultipleAlignmentEnsemble parent) {
		this.parent = parent;
	}

	@Override
	public List getAlignResCounts() {

		if (alignResCounts != null)
			return alignResCounts;

		alignResCounts = new ArrayList<>(size());
		for (int s = 0; s < size(); s++)
			alignResCounts.add(0);

		for (BlockSet bs : blockSets) {
			List bscounts = bs.getAlignResCounts();
			for (int s = 0; s < size(); s++)
				alignResCounts.set(s, alignResCounts.get(s) + bscounts.get(s));
		}
		return alignResCounts;
	}

	@Override
	public List getCoverages() {

		if (coverages != null)
			return coverages;

		List counts = getAlignResCounts();
		coverages = new ArrayList<>(size());
		for (int s = 0; s < size(); s++)
			coverages.add(counts.get(s)
					/ (double) getAtomArrays().get(s).length);
		return coverages;
	}

}