public void SuffixTreeSimpleCharSet4Text21WithStep()
{
// arrange
int step = 9879;
int bufferSize = 1000;
int textLength = 21;
char[] alphabet = new char[] { 'a', 'c', 'g', 't' };
SuffixTreeAccumulator statisticAccumulator = new SuffixTreeAccumulator(new SuffixTreeSaver(), BruteForceStringCompare.AlgorythmName,
textLength, bufferSize, alphabet.Length);
statisticAccumulator.Delete();
int size = textLength;
long max = 1L << (2 * size);
long sequenceAsNumber = 0;
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();
string text = new string(charSequence);
SuffixTreeSimple suffixTreeSimple = new SuffixTreeSimple()
{
StatisticAccumulator = statisticAccumulator
};
// act
suffixTreeSimple.Execute(text);
}
statisticAccumulator.SaveRemain();
// assert
}
public void SuffixTreeSimpleVariant3()
{
// arrange
string text = "aaaca";
string expectedTree = "[0-0]([0-0]([5-5](),[1-1]([2-5](),[3-5]()),[3-5]()),[3-5]())";
SuffixTreeSimple suffixTree = new SuffixTreeSimple()
{
StatisticAccumulator = new FakeSuffixTreeAccumulator()
};
// act
suffixTree.Execute(text);
// assert
var result = suffixTree.NodePresentationAsString();
Assert.AreEqual(result, expectedTree, "Wrong tree.");
}
//--------------------------------------------------------------------------------------
protected override bool MakeAction()
{
if (_fCurrentPosition == _fSize - 1 && --_stepCounter == 0)
{
string text = new string(_fCurrentSet.Select(i => _charSet[i]).ToArray());
SuffixTreeSimple suffixTreeSimple = new SuffixTreeSimple()
{
StatisticAccumulator = _statisticAccumulator
};
// act
suffixTreeSimple.Execute(text);
// assert
_stepCounter = _step;
}
return(false);
}
