public void ValidateSparseSequenceGetSubSequence()
{
var byteList = new List <byte>
{
Alphabets.DNA.Gap,
Alphabets.DNA.G,
Alphabets.DNA.A,
Alphabets.DNA.Gap,
Alphabets.DNA.T,
Alphabets.DNA.C,
Alphabets.DNA.Gap,
Alphabets.DNA.Gap
};
var sparseSeq = new SparseSequence(Alphabets.DNA, 0, byteList);
ISequence result = sparseSeq.GetSubSequence(0, 3);
Assert.AreEqual(3, result.Count);
Assert.AreEqual(Alphabets.DNA.Gap, result[0]);
Assert.AreEqual(Alphabets.DNA.G, result[1]);
Assert.AreEqual(Alphabets.DNA.A, result[2]);
result = sparseSeq.GetSubSequence(0, 0);
Assert.AreEqual(0, result.Count);
result = sparseSeq.GetSubSequence(3, 2);
Assert.AreEqual(2, result.Count);
Assert.AreEqual(Alphabets.DNA.Gap, result[0]);
Assert.AreEqual(Alphabets.DNA.T, result[1]);
ApplicationLog.WriteLine("SparseSequenceBVT: Validation of GetSubSequence() method successfully completed");
}
public void TestSparseSequenceGetSubsequence()
{
List <byte> byteList = new List <byte>();
byteList.Add(Alphabets.DNA.Gap);
byteList.Add(Alphabets.DNA.G);
byteList.Add(Alphabets.DNA.A);
byteList.Add(Alphabets.DNA.Gap);
byteList.Add(Alphabets.DNA.T);
byteList.Add(Alphabets.DNA.C);
byteList.Add(Alphabets.DNA.Gap);
byteList.Add(Alphabets.DNA.Gap);
SparseSequence sparseSeq = new SparseSequence(Alphabets.DNA, 0, byteList);
ISequence result = sparseSeq.GetSubSequence(0, 3);
Assert.AreEqual(3, result.Count);
Assert.AreEqual(Alphabets.DNA.Gap, result[0]);
Assert.AreEqual(Alphabets.DNA.G, result[1]);
Assert.AreEqual(Alphabets.DNA.A, result[2]);
result = sparseSeq.GetSubSequence(0, 0);
Assert.AreEqual(0, result.Count);
result = sparseSeq.GetSubSequence(3, 2);
Assert.AreEqual(2, result.Count);
Assert.AreEqual(Alphabets.DNA.Gap, result[0]);
Assert.AreEqual(Alphabets.DNA.T, result[1]);
// Invalid Argument tests.
try
{
sparseSeq.GetSubSequence(10, 10);
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
}
try
{
sparseSeq.GetSubSequence(0, 9);
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
}
try
{
sparseSeq.GetSubSequence(1, 8);
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
}
}
public void ValidateExceptionByPassingInvalidStartIndex()
{
//Create a sparse sequence.
var sparseSeq = new SparseSequence(Alphabets.DNA);
// Try to add RNA Sequence Item to DNA sparse sequence.
try
{
sparseSeq.GetSubSequence(10, 0);
Assert.Fail();
}
catch (ArgumentException)
{
ApplicationLog.WriteLine("SparseSequence P2: SparseSequence Exception was validated successfully");
}
}
public void ValidateExceptionByPassingInvalidLength()
{
//Create a sparse sequence.
var sparseSeq = new SparseSequence(Alphabets.DNA, 5);
try
{
sparseSeq.GetSubSequence(0, 10);
Assert.Fail();
}
catch (ArgumentException)
{
// Log to GUI.
ApplicationLog.WriteLine("SparseSequence P2: SparseSequence Exception was validated successfully");
}
}
public void TestSparseSequenceConstructorWithSequenceArgument()
{
IEnumerable <byte> seqItems = new List <Byte>()
{
65, 65, 67, 67
};
SparseSequence sparseSeq = new SparseSequence(Alphabets.DNA, 0, seqItems);
ISequence seq = sparseSeq.GetSubSequence(0, sparseSeq.Count);
SparseSequence newSparseSequence = new SparseSequence(seq);
ISequence newSeq = newSparseSequence.GetSubSequence(0, newSparseSequence.Count);
string expectedValue = "AACC";
string actualValue = new string(newSeq.Select(x => (char)x).ToArray());
Assert.AreEqual(expectedValue, actualValue);
}
public void ValidateExceptionByPassingInvalidLength()
{
//Create a sparse sequence.
var sparseSeq = new SparseSequence(Alphabets.DNA, 5);
try
{
sparseSeq.GetSubSequence(0, 10);
Assert.Fail();
}
catch (ArgumentException)
{
// Log to GUI.
ApplicationLog.WriteLine("SparseSequence P2: SparseSequence Exception was validated successfully");
}
}
public void ValidateExceptionByPassingInvalidStartIndex()
{
//Create a sparse sequence.
var sparseSeq = new SparseSequence(Alphabets.DNA);
// Try to add RNA Sequence Item to DNA sparse sequence.
try
{
sparseSeq.GetSubSequence(10, 0);
Assert.Fail();
}
catch (ArgumentException)
{
ApplicationLog.WriteLine("SparseSequence P2: SparseSequence Exception was validated successfully");
}
}
public void ValidateSparseSequenceGetSubSequence()
{
var byteList = new List<byte>
{
Alphabets.DNA.Gap,
Alphabets.DNA.G,
Alphabets.DNA.A,
Alphabets.DNA.Gap,
Alphabets.DNA.T,
Alphabets.DNA.C,
Alphabets.DNA.Gap,
Alphabets.DNA.Gap
};
var sparseSeq = new SparseSequence(Alphabets.DNA, 0, byteList);
ISequence result = sparseSeq.GetSubSequence(0, 3);
Assert.AreEqual(3, result.Count);
Assert.AreEqual(Alphabets.DNA.Gap, result[0]);
Assert.AreEqual(Alphabets.DNA.G, result[1]);
Assert.AreEqual(Alphabets.DNA.A, result[2]);
result = sparseSeq.GetSubSequence(0, 0);
Assert.AreEqual(0, result.Count);
result = sparseSeq.GetSubSequence(3, 2);
Assert.AreEqual(2, result.Count);
Assert.AreEqual(Alphabets.DNA.Gap, result[0]);
Assert.AreEqual(Alphabets.DNA.T, result[1]);
ApplicationLog.WriteLine("SparseSequenceBVT: Validation of GetSubSequence() method successfully completed");
}
public void TestSparseSequenceConstructorWithSequenceArgument()
{
IEnumerable<byte> seqItems = new List<Byte>() { 65, 65, 67, 67 };
SparseSequence sparseSeq = new SparseSequence(Alphabets.DNA, 0, seqItems);
ISequence seq = sparseSeq.GetSubSequence(0, sparseSeq.Count);
SparseSequence newSparseSequence = new SparseSequence(seq);
ISequence newSeq = newSparseSequence.GetSubSequence(0, newSparseSequence.Count);
string expectedValue = "AACC";
string actualValue = new string(newSeq.Select(x => (char)x).ToArray());
Assert.AreEqual(expectedValue, actualValue);
}
