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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;

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

import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
 * An internal utility class for StructureImpl to make it easier to manage poly and nonpoly chains.
 * Not to exposed to users through API.
 *
 * Created by andreas on 5/3/16.
 * @author Andreas Prlic
 * @since 5.0
 */
public class Model implements Serializable {

	private static final long serialVersionUID = 5320613424668781882L;

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

	private List polyChains;
	private List nonPolyChains;
	private List waterChains;

	public Model(){
		polyChains = new ArrayList<>();
		nonPolyChains = new ArrayList<>();
		waterChains = new ArrayList<>();
	}

	public List getPolyChains() {
		return polyChains;
	}

	public List getNonPolyChains() {
		return nonPolyChains;
	}

	public List getWaterChains() {
		return waterChains;
	}

	/**
	 * Get all chains: polymeric, non-polymeric and water
	 * @return
	 */
	public List getChains(){
		ArrayList chains = new ArrayList<>();

		chains.addAll(polyChains);
		chains.addAll(nonPolyChains);
		chains.addAll(waterChains);

		chains.trimToSize();

		return chains;
	}

	public void setChains(List modelChains) {

		polyChains.clear();
		nonPolyChains.clear();
		waterChains.clear();

		for (Chain c : modelChains){
			addChain(c);
		}
	}

	public void addChain(Chain c) {
		EntityInfo info = c.getEntityInfo();

		if ( info == null || info.getType() == null) {
			logger.info("No entity info could be found while adding chain with asym id {} (author id {}). Will consider it a polymer chain.", c.getId(), c.getName());
			polyChains.add(c);

		} else if ( info.getType() == EntityType.POLYMER) {
			polyChains.add(c);

		} else if (info.getType() == EntityType.NONPOLYMER) {
			nonPolyChains.add(c);

		} else if (info.getType() == EntityType.WATER) {
			waterChains.add(c);

		} else if (info.getType() == EntityType.MACROLIDE) {
			logger.warn("Chain with asym id {} (author id {}) has entity type 'macrolide', considering it non-polymeric", c.getId(), c.getName());
			nonPolyChains.add(c);

		} else if (info.getType() == EntityType.BRANCHED) {
			logger.warn("Chain with asym id {} (author id {}) has entity type 'branched', considering it non-polymeric", c.getId(), c.getName());
			nonPolyChains.add(c);

		} else {
			logger.warn("Chain with asym id {} (author id {}) has unsupported entity type '{}'. Will not add it to the Structure.", c.getId(), c.getName(), info.getType().toString());
			// ignore it

		}
	}

	/**
	 * Returns the total number of chains in this model: polymeric, non-polymeric and water
	 * @return
	 */
	public int size() {
		return polyChains.size() + nonPolyChains.size() + waterChains.size();
	}

	@Override
	public String toString() {
		return "["+polyChains.size()+" poly chains, "+nonPolyChains.size()+" non-poly chains, "+waterChains.size()+" water chains]";
	}
}