Index: /branches/autoquest-core-tasktrees-alignment-test/src/test/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/NumberSequenceTest.java =================================================================== --- /branches/autoquest-core-tasktrees-alignment-test/src/test/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/NumberSequenceTest.java (revision 1648) +++ /branches/autoquest-core-tasktrees-alignment-test/src/test/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/NumberSequenceTest.java (revision 1649) @@ -21,5 +21,12 @@ 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}; @@ -34,7 +41,7 @@ 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); @@ -43,14 +50,24 @@ 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()); + } Index: /branches/autoquest-core-tasktrees-alignment-test/src/test/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeatedTest.java =================================================================== --- /branches/autoquest-core-tasktrees-alignment-test/src/test/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeatedTest.java (revision 1648) +++ /branches/autoquest-core-tasktrees-alignment-test/src/test/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeatedTest.java (revision 1649) @@ -5,30 +5,93 @@ 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); + + } } Index: anches/autoquest-core-tasktrees-alignment-test/src/test/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/TaskInstanceTrieTest.java =================================================================== --- /branches/autoquest-core-tasktrees-alignment-test/src/test/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/TaskInstanceTrieTest.java (revision 1648) +++ (revision ) @@ -1,1712 +1,0 @@ -// Copyright 2012 Georg-August-Universität Göttingen, Germany -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -package de.ugoe.cs.autoquest.tasktrees.temporalrelation; - -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collection; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -import org.junit.*; - -import de.ugoe.cs.autoquest.tasktrees.TaskTreeDecoder; -import de.ugoe.cs.autoquest.tasktrees.taskequality.TaskEquality; -import de.ugoe.cs.autoquest.tasktrees.treeifc.ITaskBuilder; -import de.ugoe.cs.autoquest.tasktrees.treeifc.ITaskFactory; -import de.ugoe.cs.autoquest.tasktrees.treeifc.ITaskInstance; -import de.ugoe.cs.autoquest.tasktrees.treeifc.IUserSession; -import de.ugoe.cs.autoquest.tasktrees.treeimpl.TaskBuilder; -import de.ugoe.cs.autoquest.tasktrees.treeimpl.TaskFactory; -import de.ugoe.cs.autoquest.usageprofiles.TrieProcessor; - -import static org.junit.Assert.*; - -/** - * The class TaskInstanceTrieTest contains tests for the class - * {@link TaskInstanceTrie}. - * - * @author Patrick Harms - * @version 1.0 - */ -public class TaskInstanceTrieTest { - - /** */ - private ITaskBuilder taskBuilder = new TaskBuilder(); - - /** */ - private ITaskFactory taskFactory = new TaskFactory(); - - /** */ - private TaskTreeDecoder decoder = new TaskTreeDecoder(taskFactory, taskBuilder); - - /** */ - private TaskHandlingStrategy strategy = - new TaskHandlingStrategy(TaskEquality.IDENTICAL); - - /** */ - private IUserSession session = (IUserSession) decoder.decode - ("UserSession {" + - " Event actionA {}" + - " Event actionB {}" + - " Event actionR {}" + - " Event actionA {}" + - " Event actionC {}" + - " Event actionA {}" + - " Event actionD {}" + - " Event actionA {}" + - " Event actionB {}" + - " Event actionR {}" + - " Event actionA {}" + - "}"); - - /** - * - */ - private static void assertCollectionContent(Collection c1, Collection c2) { - assertEquals(c1.size(), c2.size()); - for (Object obj : c1) { - assertTrue(c2.contains(obj)); - } - } - - @Test - public void testTaskInstanceTaskInstanceTrie_1() throws Exception { - TaskInstanceTrie result = new TaskInstanceTrie(strategy); - - assertNotNull(result); - assertEquals(0, result.getNumLeafs()); - assertEquals(0, result.getNumSymbols()); - assertEquals(0, result.getNumLeafAncestors()); - assertTrue(result.getKnownSymbols().isEmpty()); - } - - @Test(expected = java.lang.IllegalArgumentException.class) - public void testTaskInstanceTrie_2() throws Exception { - new TaskInstanceTrie((TaskHandlingStrategy) null); - } - - @Test - public void testTrainSessions_1() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - IUserSession session = (IUserSession) decoder.decode - ("UserSession {" + - " Event action1 {}" + - " Event action2 {}" + - " Event action3 {}" + - " Event action4 {}" + - "}"); - - fixture.trainSessions(Arrays.asList(session), 2); - - assertEquals(1, fixture.getCount(Arrays.asList(session.get(0)))); - assertEquals(1, fixture.getCount(Arrays.asList(session.get(1)))); - assertEquals(1, fixture.getCount(Arrays.asList(session.get(2)))); - - // subsequences of length 1 are not trained. So for the single item sequence of the last - // task, the count must be 0 - assertEquals(0, fixture.getCount(Arrays.asList(session.get(3)))); - - - assertEquals(1, fixture.getCount(Arrays.asList(session.get(0), session.get(1)))); - assertEquals(1, fixture.getCount(Arrays.asList(session.get(1), session.get(2)))); - assertEquals(1, fixture.getCount(Arrays.asList(session.get(2), session.get(3)))); - - // this must return 0 as we only trained shorter sequences - assertEquals(0, fixture.getCount(Arrays.asList(session.get(0), session.get(1), - session.get(2)))); - - // subsequences of length 1 are not trained. So the single item sequence of the last - // task, is not counted - assertEquals(3, fixture.getNumSymbols()); - } - - @Test - public void testTrainSessions_2() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - IUserSession session = (IUserSession) decoder.decode - ("UserSession {" + - " Event action1 {}" + - " Event action1 {}" + - " Event action1 {}" + - " Event action1 {}" + - "}"); - - fixture.trainSessions(Arrays.asList(session), 2); - - for (int i = 0; i < session.size(); i++) { - // subsequences of length 1 are not trained. So the single item sequence of the last - // task is not counted. Therefore, the result must be 3 - assertEquals(3, fixture.getCount(Arrays.asList(session.get(i)))); - - for (int j = 0; j < session.size(); j++) { - assertEquals(3, fixture.getCount(Arrays.asList(session.get(i), session.get(j)))); - } - } - - // this must return 0 as we only trained shorter sequences - assertEquals(0, fixture.getCount(Arrays.asList(session.get(0), session.get(1), - session.get(2)))); - - assertEquals(1, fixture.getNumSymbols()); - } - - @Test - public void testTrainSessions_3() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - IUserSession session = (IUserSession) decoder.decode - ("UserSession {" + - " Event action1 {}" + - " Event action2 {}" + - " Event action1 {}" + - " Event action2 {}" + - "}"); - - fixture.trainSessions(Arrays.asList(session), 2); - - // subsequences of length 1 are not trained. So the single item sequence of the last - // task is not counted. Therefore, the result must be 3 - assertEquals(2, fixture.getCount(Arrays.asList(session.get(0)))); - assertEquals(1, fixture.getCount(Arrays.asList(session.get(1)))); - assertEquals(2, fixture.getCount(Arrays.asList(session.get(2)))); - assertEquals(1, fixture.getCount(Arrays.asList(session.get(3)))); - - assertEquals(2, fixture.getCount(Arrays.asList(session.get(0), session.get(1)))); - assertEquals(1, fixture.getCount(Arrays.asList(session.get(1), session.get(2)))); - assertEquals(2, fixture.getCount(Arrays.asList(session.get(2), session.get(3)))); - - // this must return 0 as we only trained shorter sequences - assertEquals(0, fixture.getCount(Arrays.asList(session.get(0), session.get(1), - session.get(2)))); - - assertEquals(2, fixture.getNumSymbols()); - } - - @Test - public void testTrainSessions_4() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - IUserSession session = (IUserSession) decoder.decode - ("UserSession {" + - " Event action1 {}" + - " Event action2 {}" + - " Event action3 {}" + - " Event action4 {}" + - "}"); - - fixture.trainSessions(Arrays.asList(session), 3); - - assertEquals(1, fixture.getCount(Arrays.asList(session.get(0)))); - assertEquals(1, fixture.getCount(Arrays.asList(session.get(1)))); - assertEquals(1, fixture.getCount(Arrays.asList(session.get(2)))); - - // subsequences of length 1 are not trained. So for the single item sequence of the last - // task, the count must be 0 - assertEquals(0, fixture.getCount(Arrays.asList(session.get(3)))); - - - assertEquals(1, fixture.getCount(Arrays.asList(session.get(0), session.get(1)))); - assertEquals(1, fixture.getCount(Arrays.asList(session.get(1), session.get(2)))); - assertEquals(1, fixture.getCount(Arrays.asList(session.get(2), session.get(3)))); - - assertEquals(1, fixture.getCount(Arrays.asList(session.get(0), session.get(1), - session.get(2)))); - assertEquals(1, fixture.getCount(Arrays.asList(session.get(1), session.get(2), - session.get(3)))); - - // we only trained shorter sequences, so we expect a count of 0 for longer ones - assertEquals(0, fixture.getCount(Arrays.asList(session.get(0), session.get(1), - session.get(2), session.get(3)))); - - // subsequences of length 1 are not trained. So the single item sequence of the last - // task, is not counted - assertEquals(3, fixture.getNumSymbols()); - } - - @Test - public void testTrainSessions_5() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - IUserSession session = (IUserSession) decoder.decode - ("UserSession {" + - " Event action1 {}" + - " Event action1 {}" + - " Event action1 {}" + - " Event action1 {}" + - "}"); - - fixture.trainSessions(Arrays.asList(session), 3); - - for (int i = 0; i < session.size(); i++) { - // subsequences of length 1 are not trained. So the single item sequence of the last - // task is not counted. Therefore, the result must be 3 - assertEquals(3, fixture.getCount(Arrays.asList(session.get(i)))); - - for (int j = 0; j < session.size(); j++) { - assertEquals(3, fixture.getCount(Arrays.asList(session.get(i), session.get(j)))); - - for (int k = 0; k < session.size(); k++) { - assertEquals(2, fixture.getCount(Arrays.asList(session.get(i), session.get(j), - session.get(k)))); - } - } - } - - // we only trained shorter sequences, so we expect a count of 0 for longer ones - assertEquals(0, fixture.getCount(Arrays.asList(session.get(0), session.get(1), - session.get(2), session.get(3)))); - - assertEquals(1, fixture.getNumSymbols()); - } - - @Test - public void testTrainSessions_6() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - IUserSession session = (IUserSession) decoder.decode - ("UserSession {" + - " Event action1 {}" + - " Event action2 {}" + - " Event action1 {}" + - " Event action2 {}" + - "}"); - - fixture.trainSessions(Arrays.asList(session), 3); - - // subsequences of length 1 are not trained. So the single item sequence of the last - // task is not counted. Therefore, the result must be 3 - assertEquals(2, fixture.getCount(Arrays.asList(session.get(0)))); - assertEquals(1, fixture.getCount(Arrays.asList(session.get(1)))); - assertEquals(2, fixture.getCount(Arrays.asList(session.get(2)))); - assertEquals(1, fixture.getCount(Arrays.asList(session.get(3)))); - - assertEquals(2, fixture.getCount(Arrays.asList(session.get(0), session.get(1)))); - assertEquals(1, fixture.getCount(Arrays.asList(session.get(1), session.get(2)))); - assertEquals(2, fixture.getCount(Arrays.asList(session.get(2), session.get(3)))); - - assertEquals(1, fixture.getCount(Arrays.asList(session.get(0), session.get(1), - session.get(2)))); - assertEquals(1, fixture.getCount(Arrays.asList(session.get(1), session.get(2), - session.get(3)))); - - // we only trained shorter sequences, so we expect a count of 0 for longer ones - assertEquals(0, fixture.getCount(Arrays.asList(session.get(0), session.get(1), - session.get(2), session.get(3)))); - - assertEquals(2, fixture.getNumSymbols()); - } - - @Test - public void testTrainSessions_7() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - IUserSession session = (IUserSession) decoder.decode - ("UserSession {" + - " Event action1 {}" + - " Event action2 {}" + - " Event action3 {}" + - " Event action4 {}" + - "}"); - - fixture.trainSessions(Arrays.asList(session), 4); - - assertEquals(1, fixture.getCount(Arrays.asList(session.get(0)))); - assertEquals(1, fixture.getCount(Arrays.asList(session.get(1)))); - assertEquals(1, fixture.getCount(Arrays.asList(session.get(2)))); - - // subsequences of length 1 are not trained. So for the single item sequence of the last - // task, the count must be 0 - assertEquals(0, fixture.getCount(Arrays.asList(session.get(3)))); - - - assertEquals(1, fixture.getCount(Arrays.asList(session.get(0), session.get(1)))); - assertEquals(1, fixture.getCount(Arrays.asList(session.get(1), session.get(2)))); - assertEquals(1, fixture.getCount(Arrays.asList(session.get(2), session.get(3)))); - - assertEquals(1, fixture.getCount(Arrays.asList(session.get(0), session.get(1), - session.get(2)))); - assertEquals(1, fixture.getCount(Arrays.asList(session.get(1), session.get(2), - session.get(3)))); - - // we only trained shorter sequences, so we expect a count of 0 for longer ones - assertEquals(1, fixture.getCount(Arrays.asList(session.get(0), session.get(1), - session.get(2), session.get(3)))); - - // subsequences of length 1 are not trained. So the single item sequence of the last - // task, is not counted - assertEquals(3, fixture.getNumSymbols()); - } - - @Test - public void testTrainSessions_8() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - IUserSession session = (IUserSession) decoder.decode - ("UserSession {" + - " Event action1 {}" + - " Event action1 {}" + - " Event action1 {}" + - " Event action1 {}" + - "}"); - - fixture.trainSessions(Arrays.asList(session), 4); - - for (int i = 0; i < session.size(); i++) { - // subsequences of length 1 are not trained. So the single item sequence of the last - // task is not counted. Therefore, the result must be 3 - assertEquals(3, fixture.getCount(Arrays.asList(session.get(i)))); - - for (int j = 0; j < session.size(); j++) { - assertEquals(3, fixture.getCount(Arrays.asList(session.get(i), session.get(j)))); - - for (int k = 0; k < session.size(); k++) { - assertEquals(2, fixture.getCount(Arrays.asList(session.get(i), session.get(j), - session.get(k)))); - } - } - } - - // we only trained shorter sequences, so we expect a count of 0 for longer ones - assertEquals(1, fixture.getCount(Arrays.asList(session.get(0), session.get(1), - session.get(2), session.get(3)))); - - assertEquals(1, fixture.getNumSymbols()); - } - - @Test - public void testTrainSessions_9() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - IUserSession session = (IUserSession) decoder.decode - ("UserSession {" + - " Event action1 {}" + - " Event action2 {}" + - " Event action1 {}" + - " Event action2 {}" + - "}"); - - fixture.trainSessions(Arrays.asList(session), 4); - - // subsequences of length 1 are not trained. So the single item sequence of the last - // task is not counted. Therefore, the result must be 3 - assertEquals(2, fixture.getCount(Arrays.asList(session.get(0)))); - assertEquals(1, fixture.getCount(Arrays.asList(session.get(1)))); - assertEquals(2, fixture.getCount(Arrays.asList(session.get(2)))); - assertEquals(1, fixture.getCount(Arrays.asList(session.get(3)))); - - assertEquals(2, fixture.getCount(Arrays.asList(session.get(0), session.get(1)))); - assertEquals(1, fixture.getCount(Arrays.asList(session.get(1), session.get(2)))); - assertEquals(2, fixture.getCount(Arrays.asList(session.get(2), session.get(3)))); - - assertEquals(1, fixture.getCount(Arrays.asList(session.get(0), session.get(1), - session.get(2)))); - assertEquals(1, fixture.getCount(Arrays.asList(session.get(1), session.get(2), - session.get(3)))); - - // we only trained shorter sequences, so we expect a count of 0 for longer ones - assertEquals(1, fixture.getCount(Arrays.asList(session.get(0), session.get(1), - session.get(2), session.get(3)))); - - assertEquals(2, fixture.getNumSymbols()); - } - - - @Test - public void testGetSequencesWithMostOccurrences_1() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - fixture.trainSessions(Arrays.asList(session), 3); - - // get all sequences with a minimal length of one that occur most often - Collection> result = fixture.getSequencesWithOccurrenceCount(1, 0); - - assertEquals(1, result.size()); - - List expected = new ArrayList(); - expected.add(session.get(0)); - - assertContains((List>) result, expected); - } - - @Test - public void testGetSequencesWithMostOccurrences_2() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - fixture.trainSessions(Arrays.asList(session), 3); - - // get all sequences with a minimal length of one that occur exactly once - Collection> result = fixture.getSequencesWithOccurrenceCount(1, 1); - - assertEquals(11, result.size()); - - List expected = new ArrayList(); - expected.add(session.get(2)); //r - expected.add(session.get(0)); //a - expected.add(session.get(4)); //c - // rac - assertContains((List>) result, expected); - - expected.clear(); - expected.add(session.get(0)); //a - expected.add(session.get(4)); //c - // ac - assertContains((List>) result, expected); - - expected.add(session.get(0)); //a - // aca - assertContains((List>) result, expected); - - expected.clear(); - expected.add(session.get(4)); //c - // c - assertContains((List>) result, expected); - - expected.add(session.get(0)); //a - // ca - assertContains((List>) result, expected); - - expected.add(session.get(6)); //d - // cad - assertContains((List>) result, expected); - - expected.clear(); - expected.add(session.get(0)); //a - expected.add(session.get(6)); //d - // ad - assertContains((List>) result, expected); - - expected.add(session.get(0)); //a - // ada - assertContains((List>) result, expected); - - expected.clear(); - expected.add(session.get(6)); //d - // d - assertContains((List>) result, expected); - - expected.add(session.get(0)); //a - // da - assertContains((List>) result, expected); - - expected.add(session.get(1)); //b - // dab - assertContains((List>) result, expected); - } - - @Test - public void testGetSequencesWithMostOccurrences_3() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - fixture.trainSessions(Arrays.asList(session), 3); - - // get all sequences with a minimal length of one that occur exactly twice - Collection> result = fixture.getSequencesWithOccurrenceCount(1, 2); - - assertEquals(7, result.size()); - - List expected = new ArrayList(); - expected.add(session.get(0)); //a - expected.add(session.get(1)); //b - // ab - assertContains((List>) result, expected); - - expected.add(session.get(2)); //r - // abr - assertContains((List>) result, expected); - - expected.clear(); - expected.add(session.get(1)); //b - // b - assertContains((List>) result, expected); - - expected.add(session.get(2)); //r - // br - assertContains((List>) result, expected); - - expected.add(session.get(0)); //a - // bra - assertContains((List>) result, expected); - - expected.clear(); - expected.add(session.get(2)); //r - // r - assertContains((List>) result, expected); - - expected.add(session.get(0)); //a - // ra - assertContains((List>) result, expected); - } - - @Test - public void testGetSequencesWithMostOccurrences_4() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - fixture.trainSessions(Arrays.asList(session), 3); - - // get all sequences with a minimal length of one that occur exactly three times - Collection> result = fixture.getSequencesWithOccurrenceCount(1, 3); - - assertEquals(0, result.size()); - } - - @Test - public void testGetSequencesWithMostOccurrences_5() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - fixture.trainSessions(Arrays.asList(session), 3); - - // get all sequences with a minimal length of one that occur exactly four times - Collection> result = fixture.getSequencesWithOccurrenceCount(1, 4); - - // as we did not train the last single action, we may expect the "a" action only 4 times - assertEquals(1, result.size()); - - List expected = new ArrayList(); - expected.add(session.get(0)); //a - assertContains((List>) result, expected); - } - - @Test - public void testGetSequencesWithMostOccurrences_6() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - fixture.trainSessions(Arrays.asList(session), 3); - - // get all sequences with a minimal length of one that occur exactly five times - Collection> result = fixture.getSequencesWithOccurrenceCount(1, 5); - - // as we did not train the last single action, we may expect the "a" action only 4 times - assertEquals(0, result.size()); - } - - @Test - public void testGetSequencesWithMostOccurrences_7() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - fixture.trainSessions(Arrays.asList(session), 3); - - // get all sequences with a minimal length of two that occur most often - Collection> result = fixture.getSequencesWithOccurrenceCount(2, 0); - - assertEquals(5, result.size()); - - List expected = new ArrayList(); - expected.add(session.get(0)); //a - expected.add(session.get(1)); //b - assertContains((List>) result, expected); - - expected.add(session.get(2)); //r - assertContains((List>) result, expected); - - expected.clear(); - expected.add(session.get(1)); //b - expected.add(session.get(2)); //r - assertContains((List>) result, expected); - - expected.add(session.get(0)); //a - assertContains((List>) result, expected); - - expected.clear(); - expected.add(session.get(2)); //r - expected.add(session.get(0)); //a - assertContains((List>) result, expected); - } - - @Test - public void testGetSequencesWithMostOccurrences_8() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - fixture.trainSessions(Arrays.asList(session), 3); - - // get all sequences with a minimal length of two that occur exactly once - Collection> result = fixture.getSequencesWithOccurrenceCount(2, 1); - - assertEquals(9, result.size()); - - List expected = new ArrayList(); - expected.add(session.get(2)); //r - expected.add(session.get(0)); //a - expected.add(session.get(4)); //c - // rac - assertContains((List>) result, expected); - - expected.clear(); - expected.add(session.get(0)); //a - expected.add(session.get(4)); //c - // ac - assertContains((List>) result, expected); - - expected.add(session.get(0)); //a - // aca - assertContains((List>) result, expected); - - expected.clear(); - expected.add(session.get(4)); //c - expected.add(session.get(0)); //a - // ca - assertContains((List>) result, expected); - - expected.add(session.get(6)); //d - // cad - assertContains((List>) result, expected); - - expected.clear(); - expected.add(session.get(0)); //a - expected.add(session.get(6)); //d - // ad - assertContains((List>) result, expected); - - expected.add(session.get(0)); //a - // ada - assertContains((List>) result, expected); - - expected.clear(); - expected.add(session.get(6)); //d - expected.add(session.get(0)); //a - // da - assertContains((List>) result, expected); - - expected.add(session.get(1)); //b - // dab - assertContains((List>) result, expected); - } - - @Test - public void testGetSequencesWithMostOccurrences_9() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - fixture.trainSessions(Arrays.asList(session), 3); - - // get all sequences with a minimal length of two that occur exactly twice - Collection> result = fixture.getSequencesWithOccurrenceCount(2, 2); - - assertEquals(5, result.size()); - - List expected = new ArrayList(); - expected.add(session.get(0)); //a - expected.add(session.get(1)); //b - // ab - assertContains((List>) result, expected); - - expected.add(session.get(2)); //r - // abr - assertContains((List>) result, expected); - - expected.clear(); - expected.add(session.get(1)); //b - expected.add(session.get(2)); //r - // br - assertContains((List>) result, expected); - - expected.add(session.get(0)); //a - // bra - assertContains((List>) result, expected); - - expected.clear(); - expected.add(session.get(2)); //r - expected.add(session.get(0)); //a - // ra - assertContains((List>) result, expected); - } - - @Test - public void testGetSequencesWithMostOccurrences_10() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - fixture.trainSessions(Arrays.asList(session), 3); - - // get all sequences with a minimal length of two that occur exactly three times - Collection> result = fixture.getSequencesWithOccurrenceCount(2, 3); - - assertEquals(0, result.size()); - } - - @Test - public void testGetSequencesWithMostOccurrences_11() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - fixture.trainSessions(Arrays.asList(session), 3); - - // get all sequences with a minimal length of three that occur most often - Collection> result = fixture.getSequencesWithOccurrenceCount(3, 0); - - assertEquals(2, result.size()); - - List expected = new ArrayList(); - expected.add(session.get(0)); //a - expected.add(session.get(1)); //b - expected.add(session.get(2)); //r - assertContains((List>) result, expected); - - expected.clear(); - expected.add(session.get(1)); //b - expected.add(session.get(2)); //r - expected.add(session.get(0)); //a - assertContains((List>) result, expected); - } - - @Test - public void testGetSequencesWithMostOccurrences_12() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - fixture.trainSessions(Arrays.asList(session), 3); - - // get all sequences with a minimal length of three that occur exactly once - Collection> result = fixture.getSequencesWithOccurrenceCount(3, 1); - - assertEquals(5, result.size()); - - List expected = new ArrayList(); - expected.add(session.get(2)); //r - expected.add(session.get(0)); //a - expected.add(session.get(4)); //c - // rac - assertContains((List>) result, expected); - - expected.clear(); - expected.add(session.get(0)); //a - expected.add(session.get(4)); //c - expected.add(session.get(0)); //a - // aca - assertContains((List>) result, expected); - - expected.clear(); - expected.add(session.get(4)); //c - expected.add(session.get(0)); //a - expected.add(session.get(6)); //d - // cad - assertContains((List>) result, expected); - - expected.clear(); - expected.add(session.get(0)); //a - expected.add(session.get(6)); //d - expected.add(session.get(0)); //a - // ada - assertContains((List>) result, expected); - - expected.clear(); - expected.add(session.get(6)); //d - expected.add(session.get(0)); //a - expected.add(session.get(1)); //b - // dab - assertContains((List>) result, expected); - } - - @Test - public void testGetSequencesWithMostOccurrences_13() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - fixture.trainSessions(Arrays.asList(session), 3); - - // get all sequences with a minimal length of four that occur most often - Collection> result = fixture.getSequencesWithOccurrenceCount(4, 0); - - // none of these exist, as the tree is only trained with sequences of length 3 - assertEquals(0, result.size()); - } - - @Test - public void testGetSequencesWithMostOccurrences_14() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - fixture.trainSessions(Arrays.asList(session), 3); - - // get all sequences with a minimal length of four that occur exactly once - Collection> result = fixture.getSequencesWithOccurrenceCount(4, 1); - - // none of these exist, as the tree is only trained with sequences of length 3 - assertEquals(0, result.size()); - } - - @Test - public void testGetCount_1() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - fixture.trainSessions(Arrays.asList(session), 3); - - List subSequence = new ArrayList(); - subSequence.add(session.get(0)); //a - - int result = fixture.getCount(subSequence); - - // as we did not train the last single action, we may expect the "a" action only 4 times - assertEquals(4, result); - } - - @Test - public void testGetCount_2() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - fixture.trainSessions(Arrays.asList(session), 3); - - List subSequence = new ArrayList(); - subSequence.add(session.get(0)); //a - subSequence.add(session.get(1)); //b - - int result = fixture.getCount(subSequence); - - assertEquals(2, result); - } - - @Test - public void testGetCount_3() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - fixture.trainSessions(Arrays.asList(session), 3); - - List subSequence = new ArrayList(); - subSequence.add(taskFactory.createNewTaskInstance(taskFactory.createNewSequence())); - - int result = fixture.getCount(subSequence); - - assertEquals(0, result); - } - - @Test - public void testGetCount_4() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - fixture.trainSessions(Arrays.asList(session), 3); - - List subSequence = new ArrayList(); - - int result = fixture.getCount(subSequence, session.get(0)); //a - - // as we did not train the last single action, we may expect the "a" action only 4 times - assertEquals(4, result); - } - - @Test - public void testGetCount_5() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - fixture.trainSessions(Arrays.asList(session), 3); - - List subSequence = new ArrayList(); - subSequence.add(session.get(0)); //a - subSequence.add(session.get(1)); //b - - int result = fixture.getCount(subSequence, session.get(2)); //r - - assertEquals(2, result); - } - - @Test - public void testGetCount_6() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - fixture.trainSessions(Arrays.asList(session), 3); - - List subSequence = new ArrayList(); - - int result = fixture.getCount - (subSequence, taskFactory.createNewTaskInstance(taskFactory.createNewSequence())); - - assertEquals(0, result); - } - - @Test - public void testGetFollowingSymbols_1() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - fixture.trainSessions(Arrays.asList(session), 3); - - List subSequence = new ArrayList(); - subSequence.add(session.get(0)); //a - Collection expected = new ArrayList(); - expected.add(session.get(1)); //b - expected.add(session.get(4)); //c - expected.add(session.get(6)); //d - - Collection result = fixture.getFollowingSymbols(subSequence); - - assertCollectionContent(expected, result); - } - - @Test - public void testGetFollowingSymbols_2() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - fixture.trainSessions(Arrays.asList(session), 3); - - List subSequence = new ArrayList(); - subSequence.add(session.get(0)); //a - subSequence.add(session.get(1)); //b - subSequence.add(session.get(2)); //r - - Collection result = fixture.getFollowingSymbols(subSequence); - - assertEquals(0, result.size()); - } - - @Test - public void testGetFollowingSymbols_3() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - fixture.trainSessions(Arrays.asList(session), 3); - - List subSequence = new ArrayList(); - subSequence.add(taskFactory.createNewTaskInstance(taskFactory.createNewSequence())); - - Collection result = fixture.getFollowingSymbols(subSequence); - - assertEquals(0, result.size()); - } - - @Test - public void testGetNumLeafAncestors_1() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - fixture.trainSessions(Arrays.asList(session), 3); - - int result = fixture.getNumLeafAncestors(); - - assertEquals(7, result); - } - - @Test - public void testGetNumLeafs_1() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - fixture.trainSessions(Arrays.asList(session), 3); - - int result = fixture.getNumLeafs(); - - assertEquals(7, result); - } - - @Test - public void testGetNumSymbols_1() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - fixture.trainSessions(Arrays.asList(session), 3); - - - int result = fixture.getNumSymbols(); - - assertEquals(5, result); - } - - @Test - public void testLargeTaskInstanceTrie_1() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - int order = 2; - - TaskInstanceTrieTester tester = new TaskInstanceTrieTester(3, 50, order); - - long start = System.currentTimeMillis(); - fixture.trainSessions(Arrays.asList(tester.userSession), order); - System.out.println("testing session with 50 task instances and 3 symbols took " + - (System.currentTimeMillis() - start) + "ms"); - - fixture.process(tester); - - // do not check if counts is empty, as some sequences may not be part of the reduced trie - // and may therefore not be processed by the tester. - //assertTrue(tester.counts.isEmpty()); - } - - @Test - public void testLargeTaskInstanceTrie_2() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - int order = 2; - - TaskInstanceTrieTester tester = new TaskInstanceTrieTester(3, 10000, order); - - long start = System.currentTimeMillis(); - fixture.trainSessions(Arrays.asList(tester.userSession), order); - System.out.println("testing session with 10000 task instances and 3 symbols took " + - (System.currentTimeMillis() - start) + "ms"); - - fixture.process(tester); - - // do not check if counts is empty, as some sequences may not be part of the reduced trie - // and may therefore not be processed by the tester. - //assertTrue(tester.counts.isEmpty()); - } - - @Test - public void testLargeTaskInstanceTrie_3() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - int order = 2; - - TaskInstanceTrieTester tester = new TaskInstanceTrieTester(30, 10000, order); - - long start = System.currentTimeMillis(); - fixture.trainSessions(Arrays.asList(tester.userSession), order); - System.out.println("testing session with 10000 task instances and 30 symbols took " + - (System.currentTimeMillis() - start) + "ms"); - - fixture.process(tester); - - // do not check if counts is empty, as some sequences may not be part of the reduced trie - // and may therefore not be processed by the tester. - //assertTrue(tester.counts.isEmpty()); - } - - @Test - public void testLargeTaskInstanceTrie_4() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - int order = 2; - - TaskInstanceTrieTester tester = new TaskInstanceTrieTester(300, 10000, order); - - long start = System.currentTimeMillis(); - fixture.trainSessions(Arrays.asList(tester.userSession), order); - System.out.println("testing session with 10000 task instances and 300 symbols took " + - (System.currentTimeMillis() - start) + "ms"); - - fixture.process(tester); - - // do not check if counts is empty, as some sequences may not be part of the reduced trie - // and may therefore not be processed by the tester. - //assertTrue(tester.counts.isEmpty()); - } - - @Test - public void testLargeTaskInstanceTrie_5() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - int order = 2; - - TaskInstanceTrieTester tester = new TaskInstanceTrieTester(1000, 10000, order); - - long start = System.currentTimeMillis(); - fixture.trainSessions(Arrays.asList(tester.userSession), order); - System.out.println("testing session with 10000 task instances and 1000 symbols took " + - (System.currentTimeMillis() - start) + "ms"); - - fixture.process(tester); - - // do not check if counts is empty, as some sequences may not be part of the reduced trie - // and may therefore not be processed by the tester. - //assertTrue(tester.counts.isEmpty()); - } - - @Test - public void testLargeTaskInstanceTrie_6() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - int order = 3; - - TaskInstanceTrieTester tester = new TaskInstanceTrieTester(3, 50, order); - - long start = System.currentTimeMillis(); - fixture.trainSessions(Arrays.asList(tester.userSession), order); - System.out.println("testing session with 50 task instances and 3 symbols took " + - (System.currentTimeMillis() - start) + "ms"); - - fixture.process(tester); - - // do not check if counts is empty, as some sequences may not be part of the reduced trie - // and may therefore not be processed by the tester. - //assertTrue(tester.counts.isEmpty()); - } - - @Test - public void testLargeTaskInstanceTrie_7() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - int order = 3; - - TaskInstanceTrieTester tester = new TaskInstanceTrieTester(3, 10000, order); - - long start = System.currentTimeMillis(); - fixture.trainSessions(Arrays.asList(tester.userSession), order); - System.out.println("testing session with 10000 task instances and 3 symbols took " + - (System.currentTimeMillis() - start) + "ms"); - - fixture.process(tester); - - // do not check if counts is empty, as some sequences may not be part of the reduced trie - // and may therefore not be processed by the tester. - //assertTrue(tester.counts.isEmpty()); - } - - @Test - public void testLargeTaskInstanceTrie_8() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - int order = 3; - - TaskInstanceTrieTester tester = new TaskInstanceTrieTester(30, 10000, order); - - long start = System.currentTimeMillis(); - fixture.trainSessions(Arrays.asList(tester.userSession), order); - System.out.println("testing session with 10000 task instances and 30 symbols took " + - (System.currentTimeMillis() - start) + "ms"); - - fixture.process(tester); - - // do not check if counts is empty, as some sequences may not be part of the reduced trie - // and may therefore not be processed by the tester. - //assertTrue(tester.counts.isEmpty()); - } - - @Test - public void testLargeTaskInstanceTrie_9() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - int order = 3; - - TaskInstanceTrieTester tester = new TaskInstanceTrieTester(300, 10000, order); - - long start = System.currentTimeMillis(); - fixture.trainSessions(Arrays.asList(tester.userSession), order); - System.out.println("testing session with 10000 task instances and 300 symbols took " + - (System.currentTimeMillis() - start) + "ms"); - - fixture.process(tester); - - // do not check if counts is empty, as some sequences may not be part of the reduced trie - // and may therefore not be processed by the tester. - //assertTrue(tester.counts.isEmpty()); - } - - @Test - public void testLargeTaskInstanceTrie_10() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - int order = 3; - - TaskInstanceTrieTester tester = new TaskInstanceTrieTester(1000, 10000, order); - - long start = System.currentTimeMillis(); - fixture.trainSessions(Arrays.asList(tester.userSession), order); - System.out.println("testing session with 10000 task instances and 1000 symbols took " + - (System.currentTimeMillis() - start) + "ms"); - - fixture.process(tester); - - // do not check if counts is empty, as some sequences may not be part of the reduced trie - // and may therefore not be processed by the tester. - //assertTrue(tester.counts.isEmpty()); - } - - @Test - public void testLargeTaskInstanceTrie_11() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - int order = 4; - - TaskInstanceTrieTester tester = new TaskInstanceTrieTester(3, 50, order); - - long start = System.currentTimeMillis(); - fixture.trainSessions(Arrays.asList(tester.userSession), order); - System.out.println("testing session with 50 task instances and 3 symbols took " + - (System.currentTimeMillis() - start) + "ms"); - - fixture.process(tester); - - // do not check if counts is empty, as some sequences may not be part of the reduced trie - // and may therefore not be processed by the tester. - //assertTrue(tester.counts.isEmpty()); - } - - @Test - public void testLargeTaskInstanceTrie_12() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - int order = 4; - - TaskInstanceTrieTester tester = new TaskInstanceTrieTester(3, 10000, order); - - long start = System.currentTimeMillis(); - fixture.trainSessions(Arrays.asList(tester.userSession), order); - System.out.println("testing session with 10000 task instances and 3 symbols took " + - (System.currentTimeMillis() - start) + "ms"); - - fixture.process(tester); - - // do not check if counts is empty, as some sequences may not be part of the reduced trie - // and may therefore not be processed by the tester. - //assertTrue(tester.counts.isEmpty()); - } - - @Test - public void testLargeTaskInstanceTrie_13() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - int order = 4; - - TaskInstanceTrieTester tester = new TaskInstanceTrieTester(30, 10000, order); - - long start = System.currentTimeMillis(); - fixture.trainSessions(Arrays.asList(tester.userSession), order); - System.out.println("testing session with 10000 task instances and 30 symbols took " + - (System.currentTimeMillis() - start) + "ms"); - - fixture.process(tester); - - // do not check if counts is empty, as some sequences may not be part of the reduced trie - // and may therefore not be processed by the tester. - //assertTrue(tester.counts.isEmpty()); - } - - @Test - public void testLargeTaskInstanceTrie_14() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - int order = 4; - - TaskInstanceTrieTester tester = new TaskInstanceTrieTester(300, 10000, order); - - long start = System.currentTimeMillis(); - fixture.trainSessions(Arrays.asList(tester.userSession), order); - System.out.println("testing session with 10000 task instances and 300 symbols took " + - (System.currentTimeMillis() - start) + "ms"); - - fixture.process(tester); - - // do not check if counts is empty, as some sequences may not be part of the reduced trie - // and may therefore not be processed by the tester. - //assertTrue(tester.counts.isEmpty()); - } - - @Test - public void testLargeTaskInstanceTrie_15() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - int order = 4; - - TaskInstanceTrieTester tester = new TaskInstanceTrieTester(1000, 10000, order); - - long start = System.currentTimeMillis(); - fixture.trainSessions(Arrays.asList(tester.userSession), order); - System.out.println("testing session with 10000 task instances and 1000 symbols took " + - (System.currentTimeMillis() - start) + "ms"); - - fixture.process(tester); - - // do not check if counts is empty, as some sequences may not be part of the reduced trie - // and may therefore not be processed by the tester. - //assertTrue(tester.counts.isEmpty()); - } - - @Test - public void testLargeTaskInstanceTrie_16() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - int order = 5; - - TaskInstanceTrieTester tester = new TaskInstanceTrieTester(3, 50, order); - - long start = System.currentTimeMillis(); - fixture.trainSessions(Arrays.asList(tester.userSession), order); - System.out.println("testing session with 50 task instances and 3 symbols took " + - (System.currentTimeMillis() - start) + "ms"); - - fixture.process(tester); - - // do not check if counts is empty, as some sequences may not be part of the reduced trie - // and may therefore not be processed by the tester. - //assertTrue(tester.counts.isEmpty()); - } - - @Test - public void testLargeTaskInstanceTrie_17() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - int order = 5; - - TaskInstanceTrieTester tester = new TaskInstanceTrieTester(3, 10000, order); - - long start = System.currentTimeMillis(); - fixture.trainSessions(Arrays.asList(tester.userSession), order); - System.out.println("testing session with 10000 task instances and 3 symbols took " + - (System.currentTimeMillis() - start) + "ms"); - - fixture.process(tester); - - // do not check if counts is empty, as some sequences may not be part of the reduced trie - // and may therefore not be processed by the tester. - //assertTrue(tester.counts.isEmpty()); - } - - @Test - public void testLargeTaskInstanceTrie_18() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - int order = 5; - - TaskInstanceTrieTester tester = new TaskInstanceTrieTester(30, 10000, order); - - long start = System.currentTimeMillis(); - fixture.trainSessions(Arrays.asList(tester.userSession), order); - System.out.println("testing session with 10000 task instances and 30 symbols took " + - (System.currentTimeMillis() - start) + "ms"); - - fixture.process(tester); - - // do not check if counts is empty, as some sequences may not be part of the reduced trie - // and may therefore not be processed by the tester. - //assertTrue(tester.counts.isEmpty()); - } - - @Test - public void testLargeTaskInstanceTrie_19() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - int order = 5; - - TaskInstanceTrieTester tester = new TaskInstanceTrieTester(300, 10000, order); - - long start = System.currentTimeMillis(); - fixture.trainSessions(Arrays.asList(tester.userSession), order); - System.out.println("testing session with 10000 task instances and 300 symbols took " + - (System.currentTimeMillis() - start) + "ms"); - - fixture.process(tester); - - // do not check if counts is empty, as some sequences may not be part of the reduced trie - // and may therefore not be processed by the tester. - //assertTrue(tester.counts.isEmpty()); - } - - @Test - public void testLargeTaskInstanceTrie_20() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - int order = 5; - - TaskInstanceTrieTester tester = new TaskInstanceTrieTester(1000, 10000, order); - - long start = System.currentTimeMillis(); - fixture.trainSessions(Arrays.asList(tester.userSession), order); - System.out.println("testing session with 10000 task instances and 1000 symbols took " + - (System.currentTimeMillis() - start) + "ms"); - - fixture.process(tester); - - // do not check if counts is empty, as some sequences may not be part of the reduced trie - // and may therefore not be processed by the tester. - //assertTrue(tester.counts.isEmpty()); - } - - @Test - public void testLargeTaskInstanceTrie_21() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - int order = 6; - - TaskInstanceTrieTester tester = new TaskInstanceTrieTester(3, 50, order); - - long start = System.currentTimeMillis(); - fixture.trainSessions(Arrays.asList(tester.userSession), order); - System.out.println("testing session with 50 task instances and 3 symbols took " + - (System.currentTimeMillis() - start) + "ms"); - - fixture.process(tester); - - // do not check if counts is empty, as some sequences may not be part of the reduced trie - // and may therefore not be processed by the tester. - //assertTrue(tester.counts.isEmpty()); - } - - @Test - public void testLargeTaskInstanceTrie_22() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - int order = 6; - - TaskInstanceTrieTester tester = new TaskInstanceTrieTester(3, 10000, order); - - long start = System.currentTimeMillis(); - fixture.trainSessions(Arrays.asList(tester.userSession), order); - System.out.println("testing session with 10000 task instances and 3 symbols took " + - (System.currentTimeMillis() - start) + "ms"); - - fixture.process(tester); - - // do not check if counts is empty, as some sequences may not be part of the reduced trie - // and may therefore not be processed by the tester. - //assertTrue(tester.counts.isEmpty()); - } - - @Test - public void testLargeTaskInstanceTrie_23() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - int order = 6; - - TaskInstanceTrieTester tester = new TaskInstanceTrieTester(30, 10000, order); - - long start = System.currentTimeMillis(); - fixture.trainSessions(Arrays.asList(tester.userSession), order); - System.out.println("testing session with 10000 task instances and 30 symbols took " + - (System.currentTimeMillis() - start) + "ms"); - - fixture.process(tester); - - // do not check if counts is empty, as some sequences may not be part of the reduced trie - // and may therefore not be processed by the tester. - //assertTrue(tester.counts.isEmpty()); - } - - @Test - public void testLargeTaskInstanceTrie_24() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - int order = 6; - - TaskInstanceTrieTester tester = new TaskInstanceTrieTester(300, 10000, order); - - long start = System.currentTimeMillis(); - fixture.trainSessions(Arrays.asList(tester.userSession), order); - System.out.println("testing session with 10000 task instances and 300 symbols took " + - (System.currentTimeMillis() - start) + "ms"); - - fixture.process(tester); - - // do not check if counts is empty, as some sequences may not be part of the reduced trie - // and may therefore not be processed by the tester. - //assertTrue(tester.counts.isEmpty()); - } - - @Test - public void testLargeTaskInstanceTrie_25() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - int order = 6; - - TaskInstanceTrieTester tester = new TaskInstanceTrieTester(1000, 10000, order); - - long start = System.currentTimeMillis(); - fixture.trainSessions(Arrays.asList(tester.userSession), order); - System.out.println("testing session with 10000 task instances and 1000 symbols took " + - (System.currentTimeMillis() - start) + "ms"); - - fixture.process(tester); - - // do not check if counts is empty, as some sequences may not be part of the reduced trie - // and may therefore not be processed by the tester. - //assertTrue(tester.counts.isEmpty()); - } - - @Test - public void testLargeTaskInstanceTrie_26() throws Exception { - TaskInstanceTrie fixture = new TaskInstanceTrie(strategy); - - int order = 3; - - TaskInstanceTrieTester tester = new TaskInstanceTrieTester(1000, 100000, order); - - long start = System.currentTimeMillis(); - fixture.trainSessions(Arrays.asList(tester.userSession), order); - System.out.println("testing session with 100000 task instances and 1000 symbols took " + - (System.currentTimeMillis() - start) + "ms"); - - fixture.process(tester); - - // do not check if counts is empty, as some sequences may not be part of the reduced trie - // and may therefore not be processed by the tester. - //assertTrue(tester.counts.isEmpty()); - } - - /** - * - */ - private void assertContains(List> listOfList, - List containedList) - { - boolean found = false; - for (List candidate : listOfList) { - if (candidate.size() == containedList.size()) { - found = true; - for (int i = 0; i < containedList.size(); i++) { - if (!strategy.getTaskComparator().equals(candidate.get(0), containedList.get(0))) { - found = false; - break; - } - } - - if (found) { - break; - } - } - } - - assertTrue(found); - } - - public static void main(String[] args) { - new org.junit.runner.JUnitCore().run(TaskInstanceTrieTest.class); - } - - /** - *

- * class internally used for testing large tries. - *

- * - * @author Patrick Harms - */ - private class TaskInstanceTrieTester implements TrieProcessor { - - /** - * the symbols used for testing the trie - */ - private Map symbols = new HashMap(); - - /** - * the simulated sequence - */ - private IUserSession userSession; - - /** - * the trained order of the tested trie - */ - private int maxOrder; - - /** - * the expected counts of subsequences - */ - private Map counts = new HashMap(); - - /** - * the maximal observed count of a subsequence - */ - private int maxCount = 0; - - /** - * generates a simulated sequence and thereby stores the expected counts of the - * subsequences up to max order in a map. The technique uses integer and long values - * to be efficient and to allow testing with large sequences and symbol numbers. However, - * the technique is restricted to 1024 different symbols and a maximum tree depth of 6. - * The tester is also used as a trie processor to check for any node in the tree, if the - * trie calculated the count correctly and if it did not create too many nodes. - */ - public TaskInstanceTrieTester(int noOfSymbols, int sequenceLength, int maxOrder) { - if (noOfSymbols > 1024) { - throw new IllegalArgumentException("too large number of symbols"); - } - if (maxOrder > 6) { - throw new IllegalArgumentException("too large number of symbols"); - } - - StringBuffer dummyUserSessionDef = new StringBuffer("UserSession {"); - for (int i = 0; i < noOfSymbols; i++) { - dummyUserSessionDef.append(" Event action"); - dummyUserSessionDef.append(i); - dummyUserSessionDef.append(" {}"); - } - dummyUserSessionDef.append("}"); - - IUserSession dummySession = - (IUserSession) decoder.decode(dummyUserSessionDef.toString()); - - for (int i = 0; i < dummySession.size(); i++) { - this.symbols.put(i, dummySession.get(i)); - } - - this.maxOrder = maxOrder; - - dummyUserSessionDef = new StringBuffer("UserSession {"); - int[] symbolIds = new int[sequenceLength]; - - for (int i = 0; i < sequenceLength; i++) { - int symbolIndex = (int) (Math.random() * noOfSymbols); - dummyUserSessionDef.append(" Event action"); - dummyUserSessionDef.append(symbolIndex); - dummyUserSessionDef.append(" {}"); - - symbolIds[i] = symbolIndex; - - if ((i - maxOrder + 1) >= 0) { - storeCounts(symbolIds, i - maxOrder + 1, i); - } - } - dummyUserSessionDef.append("}"); - - this.userSession = (IUserSession) decoder.decode(dummyUserSessionDef.toString()); - - for (int i = sequenceLength - maxOrder + 1; i < sequenceLength; i++) { - storeCounts(symbolIds, i, sequenceLength - 1); - } - } - - /** - *

- * stores the counts for the subsequence denoted by the start and end index (inclusive). - *

- */ - private void storeCounts(int[] sequence, int startIndex, int endIndex) { - long key = 0; - - for (int i = startIndex; i <= endIndex; i++) { - key = key << 10; - key += 1 + sequence[i]; - - Integer count = this.counts.get(key); - if (count == null) { - count = 0; - } - - //System.out.println(key + " " + (count + 1)); - - count++; - this.counts.put(key, count); - - maxCount = Math.max(count, maxCount); - } - } - - /* (non-Javadoc) - * @see de.ugoe.cs.autoquest.usageprofiles.TaskInstanceTrieProcessor#process(List, int) - */ - @Override - public TrieProcessor.Result process(List sequence, int count) { - long key = 0; - - for (ITaskInstance symbol : sequence) { - int symbolIndex = -1; - - for (Map.Entry entry : symbols.entrySet()) { - if (strategy.getTaskComparator().equals(entry.getValue(), symbol)) { - symbolIndex = entry.getKey(); - break; - } - } - - assertTrue("could not find symbol", symbolIndex > -1); - - key = key << 10; - key += 1 + symbolIndex; - } - - Integer expectedCount = this.counts.remove(key); - assertNotNull(expectedCount); - - if (count == maxCount) { - assertEquals(expectedCount.intValue(), count); - } - else { - assertTrue(count < maxCount); - } - - assertTrue(sequence.size() <= this.maxOrder); - - return TrieProcessor.Result.CONTINUE; - } - - } -} Index: /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/AlignmentAlgorithm.java =================================================================== --- /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/AlignmentAlgorithm.java (revision 1648) +++ /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/AlignmentAlgorithm.java (revision 1649) @@ -19,4 +19,6 @@ public abstract ArrayList getMatches(); + + public double getMaxScore(); void align(NumberSequence input1, NumberSequence input2, Index: /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java =================================================================== --- /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java (revision 1648) +++ /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java (revision 1649) @@ -102,5 +102,5 @@ //position of the maximal score of the previous row - for(int j = 2; j < length2;j++) { + for(int j = 2; j <= length2;j++) { if(matrix[i-1][j].getScore() > tempMax) { tempMax = matrix[i-1][j].getScore(); @@ -122,16 +122,16 @@ //The last additional score is not related to a character in the input sequence, it's the total score. Therefore we don't need to save something for it - if(i maxScore) { maxScore = matrix[i][j].getScore(); @@ -373,5 +373,5 @@ for (int i = 0; i <= length1+1; i++) { - for(int j = 0; j< length2; j++) { + for(int j = 0; j<= length2; j++) { matrix[i][j] = new MatrixEntry(); } Index: /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/DummySubstitutionMatrix.java =================================================================== --- /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/DummySubstitutionMatrix.java (revision 1649) +++ /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/DummySubstitutionMatrix.java (revision 1649) @@ -0,0 +1,24 @@ +package de.ugoe.cs.autoquest.tasktrees.alignment.matrix; + +public class DummySubstitutionMatrix implements SubstitutionMatrix { + + @Override + public double getScore(int pos1, int pos2) { + if(pos1==pos2) { + return 1; + } + else { + return 0; + } + } + + @Override + public double getGapPenalty() { + return -1; + } + + @Override + public void generate() { + } + +} Index: /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java =================================================================== --- /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java (revision 1648) +++ /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java (revision 1649) @@ -166,4 +166,6 @@ .generate(appData.getNumberSequences(), submat, 9); + + // Retrieve all matches reached a specific threshold Console.traceln(Level.INFO, "retrieving significant sequence pieces"); @@ -203,6 +205,11 @@ for (Iterator jt = startpositions.iterator(); jt .hasNext();) { + int start = jt.next(); + System.out.println("Found match "); + pattern.getFirstSequence().printSequence(); + pattern.getSecondSequence().printSequence(); + System.out.println("in sequence " + (j+1) + " at position " + start); pattern.addOccurence( - new MatchOccurence(jt.next(), j)); + new MatchOccurence(start, j)); } @@ -366,7 +373,9 @@ } appData.getNumber2Task().put(templist.getSequence()[i], taskInstance.getTask()); + + //System.out.println("TaskID: " + taskInstance.getTask().getId()+ " Numbersequence: " + templist.getSequence()[i]); } //Each NumberSequence is identified by its id, beginning to count at zero - templist.setId(appData.getNumberSequences().size()); + templist.setId(sessionNo-1); appData.getNumberSequences().add(templist); comparator.clearBuffers(); @@ -550,4 +559,13 @@ } } + for (int i =0;i