/*
 *                    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/
 *
 * Created on June 17, 2010
 * Author: Mark Chapman
 */

package org.biojava.nbio.alignment;

import org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix;
import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
import org.biojava.nbio.alignment.template.GapPenalty;
import org.biojava.nbio.alignment.template.PairwiseSequenceAligner;
import org.biojava.nbio.core.alignment.template.SequencePair;
import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
import org.biojava.nbio.core.sequence.DNASequence;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundSet;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.compound.DNACompoundSet;
import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
import org.junit.Before;
import org.junit.Test;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;

public class NeedlemanWunschTest {

	private static final double PRECISION = 0.00000001;

	private ProteinSequence query, target;
	private GapPenalty gaps;
	private SubstitutionMatrix<AminoAcidCompound> blosum62;
	private NeedlemanWunsch<ProteinSequence, AminoAcidCompound> alignment, self;

	@Before
	public void setup() throws CompoundNotFoundException {
		query = new ProteinSequence("ARND");
		target = new ProteinSequence("RDG");
		gaps = new SimpleGapPenalty(10, 1);
		blosum62 = SubstitutionMatrixHelper.getBlosum62();
		alignment = new NeedlemanWunsch<ProteinSequence, AminoAcidCompound>(query, target, gaps, blosum62);
		self = new NeedlemanWunsch<ProteinSequence, AminoAcidCompound>(query, query, gaps, blosum62);
	}

	@Test
	public void testComplex() throws Exception {

		short match = 2, gop = -5, gep = -3; // 2, 5, and 3 are coprime; -2 is the mismatch score
		SimpleSubstitutionMatrix<NucleotideCompound> mx = new SimpleSubstitutionMatrix<NucleotideCompound>(new DNACompoundSet(), match, (short)-match);

		DNASequence a = new DNASequence("CGTAT  ATATCGCGCGCGCGATATATATATCT TCTCTAAAAAAA".replaceAll(" ", ""));
		DNASequence b = new DNASequence("GGTATATATATCGCGCGCACGAT TATATATCTCTCTCTAAAAAAA".replaceAll(" ", ""));
//                                       --CGTATATATCGCGCGCGCGATATATATATCT-TCTCTAAAAAAA
//                                       GGTATATATATCGCGCGCACGAT-TATATATCTCTCTCTAAAAAAA
//  mismatches:                             ^              ^
// The two alignments should have the same score. The bottom one is the one the aligner found.

		PairwiseSequenceAligner<DNASequence, NucleotideCompound> aligner = Alignments.getPairwiseAligner(a, b, Alignments.PairwiseSequenceAlignerType.GLOBAL, new SimpleGapPenalty(gop, gep), mx);
		SequencePair<DNASequence, NucleotideCompound> pair = aligner.getPair();
		System.out.println(pair); // prints the alignment above

		int nMatches = "--CGTATATATCGCGCGCGCGATATATATATCT-TCTCTAAAAAAA".length() - 2 - 4;
		double expectedScore = nMatches * match
									   - 2 * match // there are two mismatches
									   + 3 * gop + 4 * gep; // there are 3 gap opens and either 1 or 4 extensions, depending on the def
		assertEquals(expectedScore, aligner.getScore(), 0.00000001);
	}

	@Test
	public void testNeedlemanWunsch() {
		NeedlemanWunsch<ProteinSequence, AminoAcidCompound> nw =
				new NeedlemanWunsch<ProteinSequence, AminoAcidCompound>();
		nw.setQuery(query);
		nw.setTarget(target);
		nw.setGapPenalty(gaps);
		nw.setSubstitutionMatrix(blosum62);
		assertEquals(nw.getScore(), alignment.getScore(), PRECISION);
	}

	@Test
	public void testGetQuery() {
		assertEquals(alignment.getQuery(), query);
		assertEquals(self.getQuery(), query);
	}

	@Test
	public void testGetTarget() {
		assertEquals(alignment.getTarget(), target);
		assertEquals(self.getTarget(), query);
	}

	@Test
	public void testGetGapPenalty() {
		assertEquals(alignment.getGapPenalty(), gaps);
		assertEquals(self.getGapPenalty(), gaps);
	}

	@Test
	public void testGetSubstitutionMatrix() {
		assertEquals(alignment.getSubstitutionMatrix(), blosum62);
		assertEquals(self.getSubstitutionMatrix(), blosum62);
	}

	@Test
	public void testIsStoringScoreMatrix() {
		assertFalse(alignment.isStoringScoreMatrix());
		assertFalse(self.isStoringScoreMatrix());
	}

	@Test
	public void testGetScoreMatrix() {
		int[][][] scores = alignment.getScoreMatrix();
		assertEquals(-6, scores[2][1][0]);
		scores = self.getScoreMatrix();
		assertEquals(4, scores[3][4][2]);
	}

	@Test
	public void testGetScoreMatrixAsString() {
		//System.out.println(alignment.getScoreMatrixAsString());
		//System.out.println(self.getScoreMatrixAsString());
		assertEquals(String.format(
				"Substitution%n" +
				"        R   D   G%n" +
				"    0  -\u221E  -\u221E  -\u221E%n" +
				"A  -\u221E  -1 -13 -12%n" +
				"R  -\u221E  -6  -3 -14%n" +
				"N  -\u221E -12  -5  -3%n" +
				"D  -\u221E -15  -6  -6%n" +
				"%nDeletion%n" +
				"        R   D   G%n" +
				"  -10  -\u221E  -\u221E  -\u221E%n" +
				"A -11  -\u221E  -\u221E  -\u221E%n" +
				"R -12 -12 -24 -23%n" +
				"N -13 -13 -14 -24%n" +
				"D -14 -14 -15 -14%n" +
						"%nInsertion%n" +
				"        R   D   G%n" +
				"  -10 -11 -12 -13%n" +
				"A  -\u221E  -\u221E -12 -13%n" +
				"R  -\u221E  -\u221E -17 -14%n" +
				"N  -\u221E  -\u221E -23 -16%n" +
				"D  -\u221E  -\u221E -26 -17%n"),
					 alignment.getScoreMatrixAsString());
		assertEquals(String.format(
										  "Substitution%n" +
				"        A   R   N   D%n" +
				"    0  -\u221E  -\u221E  -\u221E  -\u221E%n" +
				"A  -\u221E   4 -12 -14 -15%n" +
				"R  -\u221E -12   9  -7 -10%n" +
				"N  -\u221E -14  -7  15  -1%n" +
				"D  -\u221E -15 -10  -1  21%n" +
				"%nDeletion%n" +
				"        A   R   N   D%n" +
				"  -10  -\u221E  -\u221E  -\u221E  -\u221E%n" +
				"A -11  -\u221E  -\u221E  -\u221E  -\u221E%n" +
												  "R -12  -7 -23 -25 -26%n" +
				"N -13  -8  -2 -18 -21%n" +
				"D -14  -9  -3   4 -12%n" +
				"%nInsertion%n" +
				"        A   R   N   D%n" +
				"  -10 -11 -12 -13 -14%n" +
				"A  -\u221E  -\u221E  -7  -8  -9%n" +
				"R  -\u221E  -\u221E -23  -2  -3%n" +
				"N  -\u221E  -\u221E -25 -18   4%n" +
				"D  -\u221E  -\u221E -26 -21 -12%n"),
				self.getScoreMatrixAsString());
	}

	@Test
	public void testGetComputationTime() {
		assertTrue(alignment.getComputationTime() > 0);
		assertTrue(self.getComputationTime() > 0);
	}

	@Test
	public void testGetProfile() {
		assertEquals(String.format("ARND%n-RDG%n"), alignment.getProfile().toString());
		assertEquals(String.format("ARND%nARND%n"), self.getProfile().toString());
	}

	@Test
	public void testGetMaxScore() {
		assertEquals(21, alignment.getMaxScore(), PRECISION);
		assertEquals(21, self.getMaxScore(), PRECISION);
	}

	@Test
	public void testGetMinScore() {
		assertEquals(-27, alignment.getMinScore(), PRECISION);
		assertEquals(-28, self.getMinScore(), PRECISION);
	}

	@Test
	public void testGetScore() {
		assertEquals(-6, alignment.getScore(), PRECISION);
		assertEquals(21, self.getScore(), PRECISION);
	}

	@Test
	public void testGetPair() {
		assertEquals(String.format("ARND%n-RDG%n"), alignment.getPair().toString());
		assertEquals(String.format("ARND%nARND%n"), self.getPair().toString());
	}

	/**
	 * @author Daniel Cameron
	 */
	@Test
	public void should_align_all_anchored() throws CompoundNotFoundException {
		DNASequence query = new DNASequence("ACG", AmbiguityDNACompoundSet.getDNACompoundSet());
		DNASequence target = new DNASequence("CGT", AmbiguityDNACompoundSet.getDNACompoundSet());
		NeedlemanWunsch<DNASequence, NucleotideCompound> aligner = new NeedlemanWunsch<DNASequence, NucleotideCompound>(query, target, new SimpleGapPenalty((short)0, (short)10), SubstitutionMatrixHelper.getNuc4_4());
		aligner.setAnchors(new int[] { 0, 1, 2} );
		assertEquals(String.format("ACG%nCGT%n"), aligner.getPair().toString());
	}

	/**
	 * @author Daniel Cameron
	 */
	@Test
	public void should_align_starting_anchor() throws CompoundNotFoundException {
		DNASequence query = new DNASequence("AAT", AmbiguityDNACompoundSet.getDNACompoundSet());
		DNASequence target = new DNASequence("AATT", AmbiguityDNACompoundSet.getDNACompoundSet());
		NeedlemanWunsch<DNASequence, NucleotideCompound> aligner = new NeedlemanWunsch<DNASequence, NucleotideCompound>(query, target, new SimpleGapPenalty((short)0, (short)10), SubstitutionMatrixHelper.getNuc4_4());
		aligner.setAnchors(new int[] { 1, -1, -1} );
		assertEquals(String.format("-AAT%nAATT%n"), aligner.getPair().toString());
	}

	/**
	 * @author Daniel Cameron
	 */
	@Test
	public void should_align_ending_anchor() throws CompoundNotFoundException {
		DNASequence query = new DNASequence("AAG", AmbiguityDNACompoundSet.getDNACompoundSet());
		DNASequence target = new DNASequence("AATT", AmbiguityDNACompoundSet.getDNACompoundSet());
		NeedlemanWunsch<DNASequence, NucleotideCompound> aligner = new NeedlemanWunsch<DNASequence, NucleotideCompound>(query, target, new SimpleGapPenalty((short)0, (short)10), SubstitutionMatrixHelper.getNuc4_4());
		aligner.addAnchor(2, 3);
		assertEquals(String.format("AA-G%nAATT%n"), aligner.getPair().toString());
	}

	/**
	 * @author Daniel Cameron
	 */
	@Test
	public void should_align_middle_anchor() throws CompoundNotFoundException {
		DNASequence query = new DNASequence("ACTTT", AmbiguityDNACompoundSet.getDNACompoundSet());
		DNASequence target = new DNASequence("ACGTTT", AmbiguityDNACompoundSet.getDNACompoundSet());
		NeedlemanWunsch<DNASequence, NucleotideCompound> aligner = new NeedlemanWunsch<DNASequence, NucleotideCompound>(query, target, new SimpleGapPenalty((short)0, (short)10), SubstitutionMatrixHelper.getNuc4_4());
		aligner.setAnchors(new int[] { -1, 2, -1} );
		assertEquals(String.format("A-CTTT%nACGTTT%n"), aligner.getPair().toString());
	}

	/**
	 * @author Daniel Cameron
	 */
	@Test
	public void should_align_multiple_anchors() throws CompoundNotFoundException {
		DNASequence query = new DNASequence("ACGT", AmbiguityDNACompoundSet.getDNACompoundSet());
		DNASequence target = new DNASequence("ATACGT", AmbiguityDNACompoundSet.getDNACompoundSet());
		NeedlemanWunsch<DNASequence, NucleotideCompound> aligner = new NeedlemanWunsch<DNASequence, NucleotideCompound>(query, target, new SimpleGapPenalty((short)0, (short)10), SubstitutionMatrixHelper.getNuc4_4());
		aligner.addAnchor(0, 0);
		aligner.addAnchor(1, 1);
		aligner.addAnchor(2, 2);
		aligner.addAnchor(3, 5);
		assertEquals(String.format("ACG--T%nATACGT%n"), aligner.getPair().toString());
	}

	/**
	 * @author Daniel Cameron
	 */
	@Test
	public void anchors_should_not_change_score() throws CompoundNotFoundException {
		DNASequence query = new DNASequence("ACGT", AmbiguityDNACompoundSet.getDNACompoundSet());
		DNASequence target = new DNASequence("ACGT", AmbiguityDNACompoundSet.getDNACompoundSet());
		NeedlemanWunsch<DNASequence, NucleotideCompound> aligner = new NeedlemanWunsch<DNASequence, NucleotideCompound>(query, target, new SimpleGapPenalty((short)5, (short)10), SubstitutionMatrixHelper.getNuc4_4());
		NeedlemanWunsch<DNASequence, NucleotideCompound> anchored = new NeedlemanWunsch<DNASequence, NucleotideCompound>(query, target, new SimpleGapPenalty((short)5, (short)10), SubstitutionMatrixHelper.getNuc4_4());
		anchored.addAnchor(0, 0);
		anchored.addAnchor(1, 1);
		anchored.addAnchor(2, 2);
		anchored.addAnchor(3, 3);
		assertEquals(aligner.getScore(), anchored.getScore(), PRECISION);
	}

	/**
	 * @author Daniel Cameron
	 */
	@Test
	public void testAnchoredDNAAlignment() throws CompoundNotFoundException {
		DNASequence query = new DNASequence(  "ACGTACCGGTTTT", DNACompoundSet.getDNACompoundSet());
		DNASequence target = new DNASequence("TACGTCCGGTTACGTACGTT", DNACompoundSet.getDNACompoundSet());
		NeedlemanWunsch<DNASequence, NucleotideCompound> aligner = new NeedlemanWunsch<DNASequence, NucleotideCompound>(query, target, new SimpleGapPenalty((short)5, (short)2), SubstitutionMatrixHelper.getNuc4_4());
		assertEquals(String.format("-ACGTACCGGTT-------TT%nTACGT-CCGGTTACGTACGTT%n"), aligner.getPair().toString());
	}

	/**
	 * See issue #202 in github
	 * @author Jose M Duarte
	 */
	@Test
	public void testIntOverflowBug() throws CompoundNotFoundException {

		SubstitutionMatrix<NucleotideCompound> matrix = SubstitutionMatrixHelper.getNuc4_4();
		SimpleGapPenalty gap = new SimpleGapPenalty();

		String str1 =
				" ";
		String str2 =
				"TAAAGTCTTCGATATCAGTCAACCCAAGACCTTTCGAATAGCAGCCACCAGCTCTTCTCTTTTCGACGGCTCCACCTTGTTTAGAAGATTAGCA";
		//System.out.println("Lengths: "+str1.length()+" "+str2.length());

		DNASequence target = new DNASequence(str1,
				AmbiguityDNACompoundSet.getDNACompoundSet());

		DNASequence query = new DNASequence(str2,
				AmbiguityDNACompoundSet.getDNACompoundSet());

		NeedlemanWunsch<DNASequence, NucleotideCompound> aligner =
				new NeedlemanWunsch<DNASequence, NucleotideCompound>(query, target, gap, matrix);


		//System.out.println("getScore: " + aligner.getScore());
		//System.out.println("getMaxScore: " + aligner.getMaxScore());
		//System.out.println("getMinScore: " + aligner.getMinScore());
		//System.out.println("getSimilarity: " + aligner.getSimilarity());

		assertTrue("Similarity must be positive, this must be an integer overflow bug!", aligner.getSimilarity()>0);
	}

}
