Changeset 1649 for branches/autoquest-core-tasktrees-alignment-test

Timestamp:

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

Author:

rkrimmel

Message:

Adding tests to some classes.

Location:

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

Files:

• alignment/algorithms/NumberSequenceTest.java (modified) (3 diffs)
• alignment/algorithms/SmithWatermanRepeatedTest.java (modified) (1 diff)
• temporalrelation/TaskInstanceTrieTest.java (deleted)

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

@@ -21 +21 @@
                 
                 int[] pat5 = new int[]{-1,-1,-1};
+                
                 int[] pat6 = new int[]{10,11,12};
+                
+                int[] pat7 = new int[]{8,9,10};
+                int[] pat8 = new int[]{7,6,5};
+                
+                int[] pat9 = new int[]{0};
+                int[] pat10 = new int[]{1};
                 
                 
@@ -34 +41 @@
                 Match pattern = new Match();
                 pattern.setFirstSequence(firstpattern);
-                pattern.setSecondSequence(secondpattern);
-                
+                pattern.setSecondSequence(secondpattern);               
                 assertEquals(Integer.valueOf(2),ns.containsPattern(pattern).get(0));
+                assertEquals(1,ns.containsPattern(pattern).size());
                 
                 firstpattern.setSequence(pat3);
@@ -43 +50 @@
                 assertEquals(Integer.valueOf(1),ns.containsPattern(pattern).get(0));
                 assertEquals(Integer.valueOf(5),ns.containsPattern(pattern).get(1));
+                assertEquals(2,ns.containsPattern(pattern).size());
         
                 firstpattern.setSequence(pat5);
                 secondpattern.setSequence(pat5);
-                
                 assertEquals(0,ns.containsPattern(pattern).size());
                 
                 firstpattern.setSequence(pat6);
                 secondpattern.setSequence(pat6);
+                assertEquals(0,ns.containsPattern(pattern).size());
                 
+                firstpattern.setSequence(pat7);
+                secondpattern.setSequence(pat8);
                 assertEquals(0,ns.containsPattern(pattern).size());
+                
+                firstpattern.setSequence(pat9);
+                secondpattern.setSequence(pat10);
+                assertEquals(Integer.valueOf(0),ns.containsPattern(pattern).get(0));
+                assertEquals(Integer.valueOf(1),ns.containsPattern(pattern).get(1));
+                assertEquals(2,ns.containsPattern(pattern).size());
+        
         }
 

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);
+                
+                }
 
 }