public void ExecuteTestCasepAllResultDecisionMaxAsCriteriaAccept2() { // arrange string excpectedMotif1 = "agcgt"; string excpectedMotif2 = "cgtaa"; string expectedSolutionStartPosition1 = "3,5,1"; string expectedSolutionStartPosition2 = "5,0,3"; char[][] charSets = new char[][] { "agtagcgtaa".ToArray(), "cgtgcagtgt".ToArray(), "aatcgtaacc".ToArray() }; char[] alphabet = new char[] { 'a', 'c', 'g', 't' }; int substringLength = 5; RegulatoryMotifsPatternEnumeration enumeration = new RegulatoryMotifsPatternEnumeration(alphabet, charSets, substringLength, pIsAllResult: true, pIsOptimizitaion: false, pIsSumAsCriteria: false, pAcceptibleDistance: 2) { StatisticAccumulator = new FakeRegulatoryMotifsStatisticAccumulator() }; enumeration.Execute(); // assert string solutionStartPosition = string.Join(",", enumeration.SolutionStartPosition); string motifAsString = string.Join("", enumeration.Motif); List <string> solutionStartPositions = enumeration.SolutionStartPositionList.Select(s => string.Join(",", s)).ToList(); List <string> motifsAsString = enumeration.ListOfMotif.Select(m => string.Join("", m)).ToList(); Assert.IsTrue(motifsAsString.Any(m => m == excpectedMotif1), $"Motif1 is absent."); Assert.IsTrue(motifsAsString.Any(m => m == excpectedMotif2), $"Motif2 is absent."); Assert.IsTrue(solutionStartPositions.Any(p => p == expectedSolutionStartPosition1), $"Positions1 is absent."); Assert.IsTrue(solutionStartPositions.Any(p => p == expectedSolutionStartPosition2), $"Positions2 is absent."); Assert.IsTrue(enumeration.SolutionStartPositionList.Count >= 2, $"Wrong number of solutions."); Assert.IsTrue(enumeration.ListOfMotif.Count >= 2, $"Wrong number of motifs."); }
public void ExecuteTestCasepNotAllResultOptimizationMaxAsCriteriaExpexted1() { // arrange string excpectedMotif = "agcgt"; string expectedSolutionStartPosition = "3,5,1"; int expectedResult = 1; char[][] charSets = new char[][] { new char[] { 'a', 'g', 't', 't', 'g', 'c', 'g', 't', 'a', 'a' }, new char[] { 'c', 'g', 't', 'g', 'c', 'a', 'g', 't', 'g', 't' }, new char[] { 'a', 'a', 't', 'c', 'g', 't', 'a', 'a', 'c', 'c' } }; char[] alphabet = new char[] { 'a', 'c', 'g', 't' }; int substringLength = 5; RegulatoryMotifsPatternEnumeration enumeration = new RegulatoryMotifsPatternEnumeration(alphabet, charSets, substringLength, pIsAllResult: false, pIsOptimizitaion: true, pIsSumAsCriteria: false) { StatisticAccumulator = new FakeRegulatoryMotifsStatisticAccumulator() }; // act enumeration.Execute(); // assert string solutionStartPosition = string.Join(",", enumeration.SolutionStartPosition); string motifAsString = string.Join("", enumeration.Motif); Assert.AreEqual(motifAsString, excpectedMotif, $"Motif is wrong."); Assert.AreEqual(solutionStartPosition, expectedSolutionStartPosition, $"Positions are wrong."); Assert.AreEqual(enumeration.OptimalValue, expectedResult, $"Result is wrong."); }
public void ExecuteTestCasepAllResultDecisionMaxAsCriteriaAccept0() { // arrange char[][] charSets = new char[][] { "agtagcgtaa".ToArray(), "cgtgcagtgt".ToArray(), "aatcgtaacc".ToArray() }; char[] alphabet = new char[] { 'a', 'c', 'g', 't' }; int substringLength = 5; RegulatoryMotifsPatternEnumeration enumeration = new RegulatoryMotifsPatternEnumeration(alphabet, charSets, substringLength, pIsAllResult: true, pIsOptimizitaion: false, pIsSumAsCriteria: false, pAcceptibleDistance: 0) { StatisticAccumulator = new FakeRegulatoryMotifsStatisticAccumulator() }; // act // cgtaa // cgtgc // cgtaa // agcgt // agtgt // atcgt enumeration.Execute(); // assert Assert.AreEqual(enumeration.SolutionStartPositionList.Count, 0, $"Wrong number of solutions."); Assert.AreEqual(enumeration.ListOfMotif.Count, 0, $"Wrong number of motifs."); }
public void ProcessInputDataBuAdditionTestLength7Number3Pattern4Step987() { // arrange int patternLength = 4; int acceptibleDistance = 0; bool isOptimizitaion = false; bool isSumAsCriteria = false; bool isAllResult = true; int step = 98798111; int numberOfSequence = 3; int sequenceLength = 7; var sequenceLengthes = string.Join(",", Enumerable.Repeat(sequenceLength, numberOfSequence)); var statisticAccumulator = new RegulatoryMotifsStatisticAccumulator(new RegulatoryMotifSaver(), patternLength, sequenceLengthes, isOptimizitaion, isSumAsCriteria, isAllResult, acceptibleDistance, bufferSize: 1000); statisticAccumulator.Delete("RegulatoryMotifsPatternEnumeration"); char[] alphabet = new char[] { 'a', 'c', 'g', 't' }; long max = 1L << 42; //Convert.ToInt64(Math.Pow(4,21)); long sequenceAsNumber = 0; int size = numberOfSequence * sequenceLength; int[] sequence = new int[size]; char[] charSequence = new char[size]; long[] masks = new long[size]; long mask = 3; for (int i = 0; i < size; i++) { masks[i] = mask; mask <<= 2; } // act while (sequenceAsNumber < max) { int shift = 0; for (int i = 0; i < size; i++) { sequence[i] = (int)((sequenceAsNumber & masks[i]) >> shift); shift += 2; } sequenceAsNumber += step; charSequence = sequence.Select(j => alphabet[j]).ToArray(); char[][] charSets = Enumerable.Range(0, numberOfSequence).Select(i => Enumerable.Range(0, sequenceLength).Select(j => charSequence[j * numberOfSequence + i]).ToArray()).ToArray(); RegulatoryMotifsPatternEnumeration enumeration = new RegulatoryMotifsPatternEnumeration(alphabet, charSets, patternLength, pIsAllResult: false, pIsOptimizitaion: isOptimizitaion, pIsSumAsCriteria: isSumAsCriteria, pAcceptibleDistance: acceptibleDistance) { StatisticAccumulator = statisticAccumulator }; // act enumeration.Execute(); } // assert }
public void ExecuteTestCasepAllResultOptimizationMaxAsCriteriaExpexted040_351() { // arrange string excpectedMotif1 = "aattg"; string excpectedMotif2 = "agcgt"; string excpectedMotif3 = "cgtaa"; string excpectedMotif4 = "cgtca"; string excpectedMotif5 = "cgtga"; string excpectedMotif6 = "cgtta"; string expectedSolutionStartPosition1 = "0,4,0"; string expectedSolutionStartPosition2 = "3,5,1"; string expectedSolutionStartPosition3 = "5,0,3"; int expectedResult = 1; char[][] charSets = new char[][] { "agttgcgtaa".ToArray(), "cgtgaagtgt".ToArray(), "aatcgtaacc".ToArray() }; char[] alphabet = new char[] { 'a', 'c', 'g', 't' }; int substringLength = 5; RegulatoryMotifsPatternEnumeration enumeration = new RegulatoryMotifsPatternEnumeration(alphabet, charSets, substringLength, pIsAllResult: true, pIsOptimizitaion: true, pIsSumAsCriteria: false) { StatisticAccumulator = new FakeRegulatoryMotifsStatisticAccumulator() }; // act enumeration.Execute(); // assert List <string> solutionStartPositions = enumeration.SolutionStartPositionList.Select(s => string.Join(",", s)).ToList(); List <string> motifsAsString = enumeration.ListOfMotif.Select(m => string.Join("", m)).ToList(); Assert.IsTrue(motifsAsString.Any(m => m == excpectedMotif1), $"Motif1 is absent."); Assert.IsTrue(motifsAsString.Any(m => m == excpectedMotif2), $"Motif2 is absent."); Assert.IsTrue(motifsAsString.Any(m => m == excpectedMotif3), $"Motif3 is absent."); Assert.IsTrue(motifsAsString.Any(m => m == excpectedMotif4), $"Motif3 is absent."); Assert.IsTrue(motifsAsString.Any(m => m == excpectedMotif5), $"Motif3 is absent."); Assert.IsTrue(motifsAsString.Any(m => m == excpectedMotif6), $"Motif3 is absent."); Assert.IsTrue(solutionStartPositions.Any(p => p == expectedSolutionStartPosition1), $"Positions1 is absent."); Assert.IsTrue(solutionStartPositions.Any(p => p == expectedSolutionStartPosition2), $"Positions2 is absent."); Assert.IsTrue(solutionStartPositions.Any(p => p == expectedSolutionStartPosition3), $"Positions3 is absent."); Assert.AreEqual(enumeration.OptimalValue, expectedResult, $"Result is wrong."); Assert.AreEqual(enumeration.SolutionStartPositionList.Count, 6, $"Wrong number of solutions."); }
//-------------------------------------------------------------------------------------- protected override bool MakeAction() { if (_fCurrentPosition == _fSize - 1 && --_stepCounter == 0) { var currentSequence = _fCurrentSet.Select(i => _charSet[i]).ToList(); char[][] charSets_ = Enumerable.Range(0, _numberOfSequence).Select(i => currentSequence.Skip(i * _sequenceLength).Take(_sequenceLength).ToArray()).ToArray(); int[][] indecies = Enumerable.Range(0, _numberOfSequence).Select(i => Enumerable.Range(0, _sequenceLength).Select(j => j * _numberOfSequence + i).ToArray()).ToArray(); char[][] charSets = Enumerable.Range(0, _numberOfSequence).Select(i => Enumerable.Range(0, _sequenceLength).Select(j => currentSequence[j * _numberOfSequence + i]).ToArray()).ToArray(); RegulatoryMotifsPatternEnumeration enumeration = new RegulatoryMotifsPatternEnumeration(_charSet, charSets, _patternLength, pIsAllResult: false, pIsOptimizitaion: _isOptimizitaion, pIsSumAsCriteria: _isSumAsCriteria, pAcceptibleDistance: _acceptibleDistance) { StatisticAccumulator = _statisticAccumulator }; // act enumeration.Execute(); // assert // _result.Add(string.Join(",", _fCurrentSet.Select(t => t.ToString()))); _stepCounter = _step; } return(false); }
public void ExecuteTestCasepNotAllResultOptimizationSumAsCriteriaExpexted351() { // arrange string excpectedMotif1 = "agcgt"; string excpectedMotif2 = "cgtaa"; string expectedSolutionStartPosition1 = "3,5,1"; string expectedSolutionStartPosition2 = "5,0,3"; int expectedResult = 2; char[][] charSets = new char[][] { new char[] { 'a', 'g', 't', 'a', 'g', 'c', 'g', 't', 'a', 'a' }, new char[] { 'c', 'g', 't', 'g', 'c', 'a', 'g', 't', 'g', 't' }, new char[] { 'a', 'a', 't', 'c', 'g', 't', 'a', 'a', 'c', 'c' } }; char[] alphabet = new char[] { 'a', 'c', 'g', 't' }; int substringLength = 5; RegulatoryMotifsPatternEnumeration enumeration = new RegulatoryMotifsPatternEnumeration(alphabet, charSets, substringLength, pIsAllResult: true, pIsOptimizitaion: true, pIsSumAsCriteria: true) { StatisticAccumulator = new FakeRegulatoryMotifsStatisticAccumulator() }; // act // cgtaa // cgtgc // cgtaa enumeration.Execute(); // assert string solutionStartPosition = string.Join(",", enumeration.SolutionStartPosition); string motifAsString = string.Join("", enumeration.Motif); List <string> solutionStartPositions = enumeration.SolutionStartPositionList.Select(s => string.Join(",", s)).ToList(); List <string> motifsAsString = enumeration.ListOfMotif.Select(m => string.Join("", m)).ToList(); Assert.IsTrue(motifsAsString.Any(m => m == excpectedMotif1), $"Motif1 is absent."); Assert.IsTrue(motifsAsString.Any(m => m == excpectedMotif2), $"Motif2 is absent."); Assert.IsTrue(solutionStartPositions.Any(p => p == expectedSolutionStartPosition1), $"Positions1 is absent."); Assert.IsTrue(solutionStartPositions.Any(p => p == expectedSolutionStartPosition2), $"Positions2 is absent."); Assert.AreEqual(enumeration.OptimalValue, expectedResult, $"Result is wrong."); Assert.AreEqual(enumeration.SolutionStartPositionList.Count, 2, $"Wrong number of solutions."); }