public void ExecuteTestCasepNotAllResultOptimizationSumAsCriteriaExpexted2()
{
// arrange
string excpectedMotif = "cgtaa";
string expectedSolutionStartPosition = "5,0,3";
int expectedResult = 2;
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;
RegulatoryMotifsBoundaryBranchEnumeration enumeration = new RegulatoryMotifsBoundaryBranchEnumeration(alphabet, charSets, substringLength, pIsAllResult: false, pIsOptimizitaion: true, pIsSumAsCriteria: true)
{
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 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: 10000);
statisticAccumulator.Delete("RegulatoryMotifsBoundaryBranchEnumeration");
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();
RegulatoryMotifsBoundaryBranchEnumeration enumeration = new RegulatoryMotifsBoundaryBranchEnumeration(alphabet, charSets, patternLength, pIsAllResult: false, pIsOptimizitaion: isOptimizitaion, pIsSumAsCriteria: isSumAsCriteria, pAcceptibleDistance: acceptibleDistance)
{
StatisticAccumulator = statisticAccumulator
};
// act
enumeration.Execute();
}
// assert
}
public void ExecuteTestCasepAllResultDecisionMaxAsCriteriaAccept1()
{
// arrange
string excpectedMotif1 = "agcgt";
string excpectedMotif2 = "cgtac";
string excpectedMotif3 = "cgtga";
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;
RegulatoryMotifsBoundaryBranchEnumeration enumeration = new RegulatoryMotifsBoundaryBranchEnumeration(alphabet, charSets, substringLength, pIsAllResult: true, pIsOptimizitaion: false, pIsSumAsCriteria: false, pAcceptibleDistance: 1)
{
StatisticAccumulator = new FakeRegulatoryMotifsStatisticAccumulator()
};
// act
// cgtaa
// cgtgc
// cgtaa
// agcgt
// agtgt
// atcgt
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(motifsAsString.Any(m => m == excpectedMotif3), $"Motif3 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.SolutionStartPositionList.Count, 3, $"Wrong number of solutions.");
Assert.AreEqual(enumeration.ListOfMotif.Count, 3, $"Wrong number of motifs.");
}
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[][] {
new char[] { 'a', 'g', 't', 't', 'g', 'c', 'g', 't', 'a', 'a' },
new char[] { 'c', 'g', 't', 'g', 'a', '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;
RegulatoryMotifsBoundaryBranchEnumeration enumeration = new RegulatoryMotifsBoundaryBranchEnumeration(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();
RegulatoryMotifsBoundaryBranchEnumeration enumeration = new RegulatoryMotifsBoundaryBranchEnumeration(_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);
}