public void HasNextTest()
{
int lengthCut = 3;
int step = 1;
int countSteps = 0;
var iterator = new StartIterator(chain, lengthCut, step);
while (iterator.HasNext())
{
iterator.Next();
countSteps = countSteps + 1;
}
Assert.True(countSteps == iterator.MaxShifts);
countSteps = 0;
iterator = new StartIterator(chain, lengthCut, step + 1);
while (iterator.HasNext())
{
iterator.Next();
countSteps = countSteps + 1;
}
Assert.True(countSteps == iterator.MaxShifts);
}
public void GetPositionTest()
{
int lengthCut = 2;
int step = 1;
var iterator = new StartIterator(chain, lengthCut, step);
iterator.Next();
Assert.True(iterator.CursorPosition == 0);
iterator.Next();
Assert.True(iterator.CursorPosition == 1);
for (int index = 2; index < iterator.MaxShifts; index++)
{
iterator.Next();
}
Assert.True(iterator.CursorPosition == 16);
}
/// <summary>
/// The find.
/// </summary>
/// <param name="par">
/// The par.
/// </param>
/// <returns>
/// The <see cref="T:KeyValuePair{List{String},List{Int32}}"/>.
/// </returns>
public override sealed KeyValuePair<List<string>, List<int>>? Find(ContentValues par)
{
var convoluted = (ComplexChain)par.Get(Enum.GetName(typeof(Formalism), Formalism.Sequence));
var windowLen = (int)par.Get(Enum.GetName(typeof(Parameter), Parameter.Window));
var alphabet = (FrequencyDictionary)par.Get(Enum.GetName(typeof(Formalism), Formalism.Alphabet));
var level = (double)par.Get(Enum.GetName(typeof(Parameter), Parameter.CurrentThreshold));
int scanStep = 1;
int disp = 0;
var it = new StartIterator(convoluted, windowLen, scanStep);
while (it.HasNext())
{
it.Next();
fullEntry.Add(it, disp);
}
CalculateStd(convoluted, windowLen);
return DiscardCompositeWords(alphabet, level);
}
/// <summary>
/// The find.
/// </summary>
/// <param name="par">
/// The par.
/// </param>
/// <returns>
/// The <see cref="T:KeyValuePair{List{string},List{int}}?"/>.
/// </returns>
public override sealed KeyValuePair<List<string>, List<int>>? Find(ContentValues par)
{
var convoluted = (ComplexChain)par.Get(Enum.GetName(typeof(Formalism), Formalism.Sequence));
double pbalance = (int)par.Get(Enum.GetName(typeof(Parameter), Parameter.Balance)) / 100.0;
int windowLen = (int)par.Get(Enum.GetName(typeof(Parameter), Parameter.Window));
var alphabet = (FrequencyDictionary)par.Get(Enum.GetName(typeof(Formalism), Formalism.Alphabet));
var level = (double)par.Get(Enum.GetName(typeof(Parameter), Parameter.CurrentThreshold));
int scanStep = 1;
int disp = 0;
int length = convoluted.GetLength();
fullEntry = new DataCollector();
minusOneEntry = new DataCollector();
minusTwoEntry = new DataCollector();
var it = new StartIterator(convoluted, windowLen, scanStep);
CriterionMethod criteriaCalculator = new ConvolutedCriterionMethod();
while (it.HasNext())
{
it.Next();
fullEntry.Add(it, disp);
FindLess(it);
}
CalculateStd(convoluted, pbalance, windowLen, length, criteriaCalculator);
return DiscardCompositeWords(alphabet, level);
}
public void MoveTest()
{
int length = 2;
int step = 1;
int position = 3;
var iterator = new StartIterator(chain, length, step);
iterator.Move(position);
Assert.True(iterator.CursorPosition == position);
position = 100;
iterator.Move(position);
Assert.True(iterator.CursorPosition != position);
position = chain.GetLength() / 2;
iterator.Move(position);
Assert.True(iterator.CursorPosition == position);
position = -1;
iterator.Move(position);
Assert.True(iterator.CursorPosition != position);
length = 3;
step = 2;
position = 3;
string triple = "GTG";
iterator = new StartIterator(chain, length, step);
iterator.Move(position);
iterator.Next();
Assert.AreEqual(triple, Helper.ToString(iterator.Current()));
}
public void NextTest()
{
List<string> cut;
string[] triplesForStepOne =
{
"AAC", "ACA", "CAG", "AGG", "GGT", "GTG", "TGC", "GCC", "CCC", "CCC", "CCT",
"CTT", "TTA", "TAT", "ATT", "TTT"
};
string[] triplesForStepTwo = { "AAC", "CAG", "GGT", "TGC", "CCC", "CCT", "TTA", "ATT" };
int lengthCut = 3;
int step = 1;
var iterator = new StartIterator(chain, lengthCut, step);
for (int i = 0; i < iterator.MaxShifts; i++)
{
cut = iterator.Next();
Assert.True(Helper.ToString(cut).Equals(triplesForStepOne[i]));
}
iterator = new StartIterator(chain, lengthCut, step + 1);
for (int i = 0; i < iterator.MaxShifts; i++)
{
cut = iterator.Next();
Assert.True(Helper.ToString(cut).Equals(triplesForStepTwo[i]));
}
}
