source: branches/autoquest-core-tasktrees-alignment-test/src/test/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeatedTest.java

package de.ugoe.cs.autoquest.tasktrees.alignment.algorithms;

import static org.junit.Assert.*;

import org.junit.Test;

import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.DummySubstitutionMatrix;

public class SmithWatermanRepeatedTest {

        @Test
        public void testGetMaxScore() {
                int[] seq1 = new int[]{0,1,2,3,4,5,6,7,8,9};
                int[] seq2 = new int[]{0,1,2,3,4,5,6,7,8,9};
                
                NumberSequence ns1 = new NumberSequence(10);
                NumberSequence ns2 = new NumberSequence(10);
                
                ns1.setSequence(seq1);
                ns2.setSequence(seq2);
                
                DummySubstitutionMatrix submat = new DummySubstitutionMatrix();
                
                AlignmentAlgorithm testalignment1 = AlignmentAlgorithmFactory
                                .create();
                
                assertNotNull(testalignment1);
                testalignment1.align(ns1, ns2,submat,5);

                assertTrue(testalignment1.getMaxScore()==10);
        }

        @Test
        public void testGetAlignmentScore() {
                int[] seq1 = new int[]{0,1,2,3,4,5,6,7,8,9};
                int[] seq2 = new int[]{0,1,2,3,4,5,6,7,8,9};
                
                NumberSequence ns1 = new NumberSequence(10);
                NumberSequence ns2 = new NumberSequence(10);
                
                ns1.setSequence(seq1);
                ns2.setSequence(seq2);
                
                DummySubstitutionMatrix submat = new DummySubstitutionMatrix();
                
                AlignmentAlgorithm testalignment1 = AlignmentAlgorithmFactory
                                .create();
                assertNotNull(testalignment1);
                testalignment1.align(ns1, ns2,submat,5);
                assertTrue(testalignment1.getAlignmentScore()==5);
        }

        @Test
        public void testGetMatches() {
                int[] seq1 = new int[]{0,1,2,3,4,5,6,7,8,9};
                int[] seq2 = new int[]{3,4,5,6,7};
                
                NumberSequence ns1 = new NumberSequence(10);
                NumberSequence ns2 = new NumberSequence(10);
                
                ns1.setSequence(seq1);
                ns2.setSequence(seq2);
                
                DummySubstitutionMatrix submat = new DummySubstitutionMatrix();
                
                AlignmentAlgorithm testalignment1 = AlignmentAlgorithmFactory
                                .create();
                assertNotNull(testalignment1);
                testalignment1.align(ns1, ns2,submat,4);

                
                //testalignment1.getMatches().get(0).getFirstSequence().printSequence();
                //testalignment1.getMatches().get(0).getSecondSequence().printSequence();
                
        }


        //TODO: Need a better substitution matrix to do proper testing
        @Test
        public void testAlign() {
                int[] seq1 = new int[]{0,1,2, 3, 4, 5,6,7,8,9};
                int[] seq2 = new int[]{0,1,2,10,11,12,6,7,8,9};
                
                
                NumberSequence ns1 = new NumberSequence(10);
                NumberSequence ns2 = new NumberSequence(10);
                
                ns1.setSequence(seq1);
                ns2.setSequence(seq2);
                
                DummySubstitutionMatrix submat = new DummySubstitutionMatrix();
                
                AlignmentAlgorithm testalignment1 = AlignmentAlgorithmFactory
                                .create();
                assertNotNull(testalignment1);
                testalignment1.align(ns1, ns2,submat,3);
                testalignment1.printDPMatrix();
                testalignment1.printAlignment();
                assertTrue(testalignment1.getAlignmentScore()==4.0);
                
                }

}