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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 allows for finding inter-strand base pairs that are not necessarily canonical Watson-Crick pairs.
 * The implementation of findPair is different than that of the base class.  This class does not consider intra-strand
 * base pairing and for that, the TertiaryBasePairParameters class should be used.
 * @author Luke Czapla
 * @since 5.0.0
 *
 */
public class MismatchedBasePairParameters extends BasePairParameters {

	private static final long serialVersionUID = 2837124340169886674L;

	public static final double DEFAULT_MAX_STAGGER = 2.0;
	public static final double DEFAULT_MAX_PROPELLER = 60.0;
	public static final double DEFAULT_MAX_SHEAR = 5.0;
	public static final double DEFAULT_MAX_STRETCH = 5.0;

	// These are the criteria used to select proper base pairs.
	private double maxStagger = DEFAULT_MAX_STAGGER,
			maxShear = DEFAULT_MAX_SHEAR,
			maxStretch = DEFAULT_MAX_STRETCH,
			maxPropeller = DEFAULT_MAX_PROPELLER;

	/**
	 * This constructor is used to create the TertiaryBasePairParameters object.  The parent constructors are valid
	 * as well, but for this class, it makes the most sense to specify the exact parameters for the analysis.
	 * @param structure The Structure to analyze
	 * @param RNA Whether to analyze RNA (if false, it will analyze DNA)
	 * @param removeDups Whether to remove duplicate sequences (useful for RCSB data with redundant units).
	 * @param canonical Whether to only consider canonical Watson-Crick base pairs.  If false, any pairing will be identified
	 *                  as long it falls below the maximum values of stagger, shear, and stretch.
	 */
	public MismatchedBasePairParameters(Structure structure, boolean RNA, boolean removeDups, boolean canonical) {

		super(structure, RNA, removeDups, canonical);

	}

	/**
	 * This is an implementation for finding non-canonical base pairs when there may be missing or overhanging bases.
	 * @param chains The list of chains already found to be nucleic acids.
	 * @return The list of the atom groups (residues) that are pairs, as a Pair of nucleic acid 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();
			for (int m = 0; m < sequence.length(); m++) {
				boolean foundPair = false;
				Integer type1, type2;
				for (int j = i + 1; j < chains.size() && !foundPair; j++) {
					Chain c2 = chains.get(j);
					if (j > i+1 && c.getAtomSequence().equals(c2.getAtomSequence()) && nonredundant) continue;
					String sequence2 = c2.getAtomSequence();
					for (int k = c2.getAtomSequence().length() - 1; k >= 0 && !foundPair; k--) {
						if (canonical && !BasePairParameters.match(sequence.charAt(m), sequence2.charAt(k), useRNA)) continue;
						Group g1 = c.getAtomGroup(m);
						Group g2 = c2.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;
						// similarly, extreme shear and stretch is not a good base pair
						if (Math.abs(pairParameters[3]) > maxShear) continue;
						if (Math.abs(pairParameters[4]) > maxStretch) 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(i));
					lastFoundPair = foundPair;
				}
			}
		}
		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 propeller ("propeller-twist", in degrees) 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 propeller (in Å) allowed to consider two bases paired
	 */
	public void setMaxStagger(double maxStagger) {
		this.maxStagger = maxStagger;
	}

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

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

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

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

	/**
	 * 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;
	}
}