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 EnumerateCharSetForMotifsPatternBranch(char[] pCharSet, int pSequenceLength,
int pNumberOfSequence, int pPatternLength, bool pIsAllResult,
bool pIsOptimizitaion = false, bool pIsSumAsCriteria = false,
int pAcceptibleDistance = 0, int pStep = 1)
: base(pCharSet, pSequenceLength * pNumberOfSequence, 0)
{
_patternLength = pPatternLength;
_acceptibleDistance = pAcceptibleDistance;
_isOptimizitaion = pIsOptimizitaion;
_isSumAsCriteria = pIsSumAsCriteria;
_isAllResult = pIsAllResult;
_step = pStep;
_stepCounter = 1;
_numberOfSequence = pNumberOfSequence;
_sequenceLength = pSequenceLength;
var sequenceLengthes = string.Join(",", Enumerable.Repeat(_sequenceLength, _numberOfSequence));
_statisticAccumulator = new RegulatoryMotifsStatisticAccumulator(new RegulatoryMotifSaver(), _patternLength, sequenceLengthes,
_isOptimizitaion, _isSumAsCriteria, _isAllResult, _acceptibleDistance, bufferSize: 10000);
_statisticAccumulator.Delete("RegulatoryMotifsBoundaryBranchEnumeration");
}
