public void TestComplementation()
{
ISequence seq = new Sequence(Alphabets.DNA, "GATACCCAAGGT");
ISequence complement = Complementation.Complement(seq);
Assert.AreEqual("CTATGGGTTCCA", complement.ToString());
ISequence reverseComplement = Complementation.ReverseComplement(seq);
Assert.AreEqual("ACCTTGGGTATC", reverseComplement.ToString());
}
public void ValidateRevComplementForNull()
{
bool Exthrown = false;
// Reverse Complement null Sequence.
try
{
Complementation.ReverseComplement(null);
}
catch (NullReferenceException)
{
Exthrown = true;
}
// Validate if Reverse Complement method is throwing an exception.
Assert.IsTrue(Exthrown);
ApplicationLog.WriteLine(
"Translation P2: Reverse complement method was throwing an expection for null value.");
}
public void ValidateDnaReverseComplementationWithTweleveChars()
{
// Get Node values from XML.
string alphabetName = _utilityObj._xmlUtil.GetTextValue(
Constants.SimpleDnaAlphabetNode, Constants.AlphabetNameNode);
string expectedSeq = _utilityObj._xmlUtil.GetTextValue(
Constants.ComplementNode, Constants.DnaSequence);
string expectedRevComplement = _utilityObj._xmlUtil.GetTextValue(
Constants.ComplementNode, Constants.DnaRevComplement);
ISequence seq = new Sequence(Utility.GetAlphabet(alphabetName), expectedSeq);
// Reverse Complement DNA Sequence.
ISequence revComplement = Complementation.ReverseComplement(seq);
// Validate Reverse Complement for a given sequence.
Assert.AreEqual(revComplement.ToString(), expectedRevComplement);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Translation P1: Reverse Complement {0} is expected.", revComplement));
ApplicationLog.WriteLine(
"Translation P1: Reverse Complement of twelve DNA characters sequence validated successfully.");
}
public void ValidateMoreThanTwelveCharsDnaComplementation()
{
// Get Node values from XML.
string alphabetName = _utilityObj._xmlUtil.GetTextValue(
Constants.SimpleDnaAlphabetNode, Constants.AlphabetNameNode);
string expectedSeq = _utilityObj._xmlUtil.GetTextValue(
Constants.ComplementNode, Constants.DnaSymbol);
string expectedComplement = _utilityObj._xmlUtil.GetTextValue(
Constants.ComplementNode, Constants.DnaSymbolComplement);
ISequence seq = new Sequence(Utility.GetAlphabet(alphabetName), expectedSeq);
// Complement DNA Sequence.
ISequence complement = Complementation.Complement(seq);
// Validate Complement for a given sequence.
Assert.AreEqual(complement.ToString(), expectedComplement);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Translation P1: Complement {0} is expected.", complement));
ApplicationLog.WriteLine(
"Translation P1: Complement of More than twelve DNA characters sequence was validate successfully.");
}
public void ValidateDnaRevComplementation()
{
// Get Node values from XML.
string alphabetName = Utility._xmlUtil.GetTextValue(
Constants.SimpleDnaAlphabetNode, Constants.AlphabetNameNode);
string expectedSeq = Utility._xmlUtil.GetTextValue(
Constants.ComplementNode, Constants.DnaSequence);
string expectedRevComplement = Utility._xmlUtil.GetTextValue(
Constants.ComplementNode, Constants.DnaRevComplement);
ISequence seq = new Sequence(Utility.GetAlphabet(alphabetName), expectedSeq);
// Reverse Complement of DNA Sequence.
ISequence revComplement = Complementation.ReverseComplement(seq);
// Validate Reverse Complement.
Assert.AreEqual(revComplement.ToString(), expectedRevComplement);
ApplicationLog.WriteLine(string.Format(null,
"Translation BVT: Reverse Complement {0} is expected.", seq));
ApplicationLog.WriteLine(
"Translation BVT: Reverse Complement of DNA sequence was validate successfully.");
}
public void ValidateMoreThanTwelveCharsDnaRevComplementation()
{
// Get Node values from XML.
string alphabetName = Utility._xmlUtil.GetTextValue(
Constants.SimpleDnaAlphabetNode, Constants.AlphabetNameNode);
string expectedSeq = Utility._xmlUtil.GetTextValue(
Constants.ComplementNode, Constants.DnaSequenceWithMoreThanTwelveChars);
string expectedComplement = Utility._xmlUtil.GetTextValue(
Constants.ComplementNode, Constants.DnaRevComplementForMoreThanTwelveChars);
ISequence seq = new Sequence(Utility.GetAlphabet(alphabetName), expectedSeq);
// Reverse Complement DNA Sequence.
ISequence revComplement = Complementation.ReverseComplement(seq);
// Validate Reverse Complement. for a given sequence.
Assert.AreEqual(revComplement.ToString(), expectedComplement);
ApplicationLog.WriteLine(string.Format(null,
"Translation P1: Rev Complement {0} is expected.", revComplement));
ApplicationLog.WriteLine(
"Translation P1: Reverse Complement of More than twelve DNA characters sequence was validate successfully.");
}
public void ValidateSingleDnaSymbolComplementation()
{
// Get Node values from XML.
string alphabetName = Utility._xmlUtil.GetTextValue(
Constants.SimpleDnaAlphabetNode, Constants.AlphabetNameNode);
string expectedSeq = Utility._xmlUtil.GetTextValue(
Constants.ComplementNode, Constants.DnaSymbol);
string expectedComplement = Utility._xmlUtil.GetTextValue(
Constants.ComplementNode, Constants.DnaSymbolComplement);
ISequence seq = new Sequence(Utility.GetAlphabet(alphabetName), expectedSeq);
// Complement DNA Sequence.
ISequence complement = Complementation.Complement(seq);
// Validate Single DNA Symbol Complement.
Assert.AreEqual(complement.ToString(), expectedComplement);
ApplicationLog.WriteLine(string.Format(null,
"Translation P1: Complement {0} is expected.", complement));
ApplicationLog.WriteLine(
"Translation P1: Complement of Single DNA Symbol was validate successfully.");
}
protected override ActivityExecutionStatus Execute(ActivityExecutionContext executionContext)
{
DnaOrRnaOutput = Complementation.Complement(DnaOrRnaInput);
return(ActivityExecutionStatus.Closed);
}
