Changeset 1649 for branches/autoquest-core-tasktrees-alignment-test/src/test/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeatedTest.java

Timestamp:

08/03/14 22:53:27 (10 years ago)

Author:

rkrimmel

Message:

Adding tests to some classes.

File:

• branches/autoquest-core-tasktrees-alignment-test/src/test/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeatedTest.java (modified) (1 diff)

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

@@ -5 +5 @@
 import org.junit.Test;
 
+import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.DummySubstitutionMatrix;
+
 public class SmithWatermanRepeatedTest {
 
         @Test
         public void testGetMaxScore() {
-                fail("Not yet implemented");
+                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();
+                testalignment1.align(ns1, ns2,submat,5);
+
+                assertTrue(testalignment1.getMaxScore()==10);
         }
 
         @Test
         public void testGetAlignmentScore() {
-                fail("Not yet implemented");
+                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();
+                testalignment1.align(ns1, ns2,submat,5);
+                assertTrue(testalignment1.getAlignmentScore()==5);
         }
 
         @Test
         public void testGetMatches() {
-                fail("Not yet implemented");
+                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();
+                testalignment1.align(ns1, ns2,submat,4);
+                testalignment1.printDPMatrix();
+                testalignment1.printAlignment();
+                
+                //testalignment1.getMatches().get(0).getFirstSequence().printSequence();
+                //testalignment1.getMatches().get(0).getSecondSequence().printSequence();
+                
         }
 
-        @Test
-        public void testGetAlignment() {
-                fail("Not yet implemented");
-        }
 
+        //TODO: Need a better substitution matrix to do proper testing
         @Test
         public void testAlign() {
-                fail("Not yet implemented");
-        }
+                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();
+                testalignment1.align(ns1, ns2,submat,3);
+                //assertTrue(testalignment1.getAlignmentScore()==7);
+                
+                }
 
 }