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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.basepairs;

import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.Chain;
import org.biojava.nbio.structure.Group;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.contact.Pair;

import javax.vecmath.Matrix4d;
import java.util.ArrayList;
import java.util.List;

/**
 * This class also finds the base pairing and base-pair step parameters but has a broader definition
 * of a base pair so that non-canonical-WC base pairs will be detected and reported.  This is useful
 * for RNA that has folded into different regions, and for higher-order DNA structures.  Intra-strand
 * pairings are considered in this class (but in not the base class or MismatchedBasePairParameters class)
 * @author Luke Czapla
 * @since 5.0.0
 *
 */
public class TertiaryBasePairParameters extends BasePairParameters {

	private static final long serialVersionUID = 2556427111533466577L;

	public static final double DEFAULT_MAX_STAGGER = 2.0;
	public static final double DEFAULT_MAX_PROPELLER = 60.0;
	// These are the criteria used to select proper base pairs.
	private double maxStagger = DEFAULT_MAX_STAGGER,
			maxPropeller = DEFAULT_MAX_PROPELLER;

	public TertiaryBasePairParameters(Structure structure, boolean RNA, boolean removeDups) {
		super(structure, RNA, removeDups);
	}

	/**
	 * This is an alternative implementation of findPair() that looks for anything that would fit the
	 * criteria for a base-pair, useful for the context of tertiary structure of RNA.  Intra-strand base pairs
	 * are found with this algorithm.
	 * @param chains The list of chains already found to be nucleic acids
	 * @return A list of the Pair of groups that match the base pair criteria, including intra-strand groups.
	 */
	@Override
	public List> findPairs(List chains) {
		List> result = new ArrayList<>();
		boolean lastFoundPair = false;
		for (int i = 0; i < chains.size(); i++) {
			Chain c = chains.get(i);
			String sequence = c.getAtomSequence();
			Integer type1, type2;
			for (int j = 0; j < sequence.length(); j++) {
				boolean foundPair = false;
				for (int k = sequence.length()-1; k >= j + 3 && !foundPair; k--) {
					Group g1 = c.getAtomGroup(j);
					Group g2 = c.getAtomGroup(k);
					type1 = BASE_MAP.get(g1.getPDBName());
					type2 = BASE_MAP.get(g2.getPDBName());
					if (type1 == null || type2 == null) continue;
					Atom a1 = g1.getAtom("C1'");
					Atom a2 = g2.getAtom("C1'");
					if (a1 == null || a2 == null) continue;
					// C1'-C1' distance is one useful criteria
					if (Math.abs(a1.getCoordsAsPoint3d().distance(a2.getCoordsAsPoint3d())-10.0) > 4.0) continue;
					Pair ga = new Pair<>(g1, g2);
					// TODO is this call needed?? JD 2018-03-07
					@SuppressWarnings("unused")
					Matrix4d data = basePairReferenceFrame(ga);
					// if the stagger is greater than 2 Å, it's not really paired.
					if (Math.abs(pairParameters[5]) > maxStagger) continue;
					// if the propeller is ridiculous it's also not that good of a pair.
					if (Math.abs(pairParameters[1]) > maxPropeller) {
						continue;
					}
					result.add(ga);
					pairingNames.add(useRNA ? BASE_LIST_RNA[type1]+ BASE_LIST_RNA[type2]: BASE_LIST_DNA[type1]+ BASE_LIST_DNA[type2]);
					foundPair = true;
				}
				if (!foundPair && lastFoundPair) {
					if (pairSequence.length() > 0 && pairSequence.charAt(pairSequence.length()-1) != ' ')
						pairSequence += ' ';
				}
				if (foundPair) pairSequence += (c.getAtomSequence().charAt(j));
				lastFoundPair = foundPair;
			}
		}
		result.addAll(super.findPairs(chains));
		return result;
	}

	/**
	 * This method returns the maximum stagger between bases used as criteria for the characterization of two bases as being paired.
	 * @return the maximum stagger (in Å) allowed.
	 */
	public double getMaxStagger() {
		return maxStagger;
	}

	/**
	 * This method sets the maximum stagger allowed for a base pair, prior to analyze() call
	 * @param maxStagger The maximum stagger (in Å) allowed to consider two bases paired
	 */
	public void setMaxStagger(double maxStagger) {
		this.maxStagger = maxStagger;
	}

	/**
	 * This method returns the maximum propeller twist between bases used as criteria for the characterization of two bases as being paired.
	 * @return the maximum propeller ("propeller-twist", in degrees) allowed.
	 */
	public double getMaxPropeller() {
		return maxPropeller;
	}

	/**
	 * This method sets the maximum propeller allowed for a base pair, prior to analyze() call
	 * @param maxPropeller The maximum propeller ("propeller-twist", in degrees) allowed to consider two bases paired
	 */
	public void setMaxPropeller(double maxPropeller) {
		this.maxPropeller = maxPropeller;
	}
}