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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 javax.vecmath.Matrix4d;

/**
 * A general implementation of a BlockSet to store a flexible part of a multiple
 * alignment.
 *
 * @author Aleix Lafita
 * @since 4.1.0
 *
 */
public class BlockSetImpl extends AbstractScoresCache implements Serializable,
		BlockSet, Cloneable {

	private static final long serialVersionUID = -1015791986000076089L;

	// Member variables
	private MultipleAlignment parent;
	private List blocks;

	// Cache variables (can be updated)
	private List pose; // Transformation matrices
	private int length;
	private int coreLength;
	private List alignResCounts;

	/**
	 * Constructor. Links also the parent to this instance by adding the
	 * BlockSet to the parent's List.
	 *
	 * @param alignment
	 *            MultipleAlignment parent of the BlockSet.
	 * @return BlockSet an instance linked to the parent alignment.
	 */
	public BlockSetImpl(MultipleAlignment alignment) {

		parent = alignment;
		if (parent != null)
			parent.getBlockSets().add(this);
		blocks = null;

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

	/**
	 * Copy constructor. Makes also a deep copy of all constituent {@link Block}
	 * s.
	 *
	 * @param bs
	 *            BlockSet object to be copied.
	 * @return BlockSet an identical copy of the input object.
	 */
	public BlockSetImpl(BlockSetImpl bs) {

		super(bs); // This copies the cached scores
		this.parent = bs.parent;
		this.length = bs.length;
		this.coreLength = bs.coreLength;

		this.pose = null;
		if (bs.pose != null) {
			// Make a deep copy of everything
			this.pose = new ArrayList();
			for (Matrix4d trans : bs.pose) {
				Matrix4d newTrans = (Matrix4d) trans.clone();
				pose.add(newTrans);
			}
		}

		blocks = null;
		if (bs.blocks != null) {
			// Make a deep copy of everything
			this.blocks = new ArrayList<>();
			for (Block b : bs.blocks) {
				Block newB = b.clone();
				newB.setBlockSet(this);
				this.blocks.add(newB);
			}
		}
	}

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

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

	@Override
	public String toString() {
		return "BlockSetImpl [blocks=" + blocks + ", pose=" + pose
				+ ", length=" + length + ", coreLength=" + coreLength + "]";
	}

	@Override
	public MultipleAlignment getMultipleAlignment() {
		return parent;
	}

	@Override
	public void setMultipleAlignment(MultipleAlignment parent) {
		this.parent = parent;
	}

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

	@Override
	public void setBlocks(List blocks) {
		this.blocks = blocks;
		for (Block b : blocks) {
			b.setBlockSet(this);
		}
	}

	@Override
	public List getTransformations() {
		return pose;
	}

	@Override
	public void setTransformations(List transformations) {
		if (size() != transformations.size()) {
			throw new IllegalArgumentException(
					"Wrong number of structures for this alignment");
		}
		pose = transformations;
	}

	@Override
	public int length() {
		if (length == -1)
			updateLength();
		return length;
	}

	@Override
	public int size() {
		// Get the size from the variables that can contain the information
		if (parent != null)
			return parent.size();
		else if (getBlocks().size() == 0) {
			throw new IndexOutOfBoundsException(
					"Empty BlockSet: number of Blocks == 0.");
		} else
			return blocks.get(0).size();
	}

	@Override
	public int getCoreLength() {
		if (coreLength == -1)
			updateCoreLength();
		return coreLength;
	}

	protected void updateLength() {
		if (getBlocks().size() == 0) {
			throw new IndexOutOfBoundsException(
					"Empty BlockSet: number of Blocks == 0.");
		}
		// Try to calculate it from the Block information
		else {
			length = 0;
			for (Block block : blocks)
				length += block.length();
		}
	}

	protected void updateCoreLength() {
		if (getBlocks().size() == 0) {
			throw new IndexOutOfBoundsException(
					"Empty BlockSet: number of Blocks == 0.");
		}
		// Try to calculate it from the Block information
		else {
			coreLength = 0;
			for (Block block : blocks)
				coreLength += block.getCoreLength();
		}
	}

	protected void updateCache() {
		updateCoreLength();
		updateLength();
	}

	@Override
	public List getAlignResCounts() {

		if (alignResCounts != null)
			return alignResCounts;

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

		for (Block b : blocks) {
			List bcounts = b.getAlignResCounts();
			for (int s = 0; s < size(); s++)
				alignResCounts.set(s, alignResCounts.get(s) + bcounts.get(s));
		}
		return alignResCounts;
	}

}