public void TestAmbiguousRnaAlphabetCompareSymbols()
{
AmbiguousRnaAlphabet ambiguousRnaAlphabet = AmbiguousRnaAlphabet.Instance;
Assert.AreEqual(false, ambiguousRnaAlphabet.CompareSymbols((byte)'A', (byte)'M'));
Assert.AreEqual(true, ambiguousRnaAlphabet.CompareSymbols((byte)'A', (byte)'A'));
}
public void TestAllAlphabetsToString()
{
DnaAlphabet dna = DnaAlphabet.Instance;
RnaAlphabet rna = RnaAlphabet.Instance;
ProteinAlphabet protein = ProteinAlphabet.Instance;
AmbiguousDnaAlphabet dnaAmbiguous = AmbiguousDnaAlphabet.Instance;
AmbiguousRnaAlphabet rnaAmbiguous = AmbiguousRnaAlphabet.Instance;
AmbiguousProteinAlphabet proteinAmbiguous = AmbiguousProteinAlphabet.Instance;
string dnaStringActual = dna.ToString();
string rnaStringActual = rna.ToString();
string proteinStringActual = protein.ToString();
string dnaAmbiguousStringActual = dnaAmbiguous.ToString();
string rnaAmbiguousStringActual = rnaAmbiguous.ToString();
string proteinAmbiguousStringActual = proteinAmbiguous.ToString();
string dnaStringExpected = "ACGT-";
string rnaStringExpected = "ACGU-";
string proteinStringExpected = "ACDEFGHIKLMNOPQRSTUVWY-*";
string dnaAmbiguousStringExpected = "ACGT-MRSWYKVHDBN";
string rnaAmbiguousStringExpected = "ACGU-NMRSWYKVHDB";
string proteinAmbiguousStringExpected = "ACDEFGHIKLMNOPQRSTUVWY-*XZBJ";
Assert.AreEqual(dnaStringExpected, dnaStringActual);
Assert.AreEqual(rnaStringExpected, rnaStringActual);
Assert.AreEqual(proteinStringExpected, proteinStringActual);
Assert.AreEqual(dnaAmbiguousStringExpected, dnaAmbiguousStringActual);
Assert.AreEqual(rnaAmbiguousStringExpected, rnaAmbiguousStringActual);
Assert.AreEqual(proteinAmbiguousStringExpected, proteinAmbiguousStringActual);
}
public void ValidateAmbiguousRnaAplhabet()
{
char[] ambiguousCharacters = new char[10] {
'M', 'H', 'W', 'R', 'D', 'S', 'V', 'K', 'B', 'Y'
};
AmbiguousRnaAlphabet rnaAlphabetInstance = AmbiguousRnaAlphabet.Instance;
Assert.AreEqual((char)rnaAlphabetInstance.AC, ambiguousCharacters[0]);
Assert.AreEqual((char)rnaAlphabetInstance.ACU, ambiguousCharacters[1]);
Assert.AreEqual((char)rnaAlphabetInstance.AU, ambiguousCharacters[2]);
Assert.AreEqual((char)rnaAlphabetInstance.GA, ambiguousCharacters[3]);
Assert.AreEqual((char)rnaAlphabetInstance.GAU, ambiguousCharacters[4]);
Assert.AreEqual((char)rnaAlphabetInstance.GC, ambiguousCharacters[5]);
Assert.AreEqual((char)rnaAlphabetInstance.GCA, ambiguousCharacters[6]);
Assert.AreEqual((char)rnaAlphabetInstance.GU, ambiguousCharacters[7]);
Assert.AreEqual((char)rnaAlphabetInstance.GUC, ambiguousCharacters[8]);
Assert.AreEqual((char)rnaAlphabetInstance.UC, ambiguousCharacters[9]);
ApplicationLog.WriteLine(string.Concat(@"Alphabets BVT: Validation of
Ambiguous Rna characters completed successfully."));
}
public void ValidateAllAlphabetsToString()
{
DnaAlphabet dna = DnaAlphabet.Instance;
RnaAlphabet rna = RnaAlphabet.Instance;
ProteinAlphabet protein = ProteinAlphabet.Instance;
AmbiguousDnaAlphabet dnaAmbiguous = AmbiguousDnaAlphabet.Instance;
AmbiguousRnaAlphabet rnaAmbiguous = AmbiguousRnaAlphabet.Instance;
AmbiguousProteinAlphabet proteinAmbiguous = AmbiguousProteinAlphabet.Instance;
string dnaStringActual = dna.ToString();
string rnaStringActual = rna.ToString();
string proteinStringActual = protein.ToString();
string dnaAmbiguousStringActual = dnaAmbiguous.ToString();
string rnaAmbiguousStringActual = rnaAmbiguous.ToString();
string proteinAmbiguousStringActual = proteinAmbiguous.ToString();
Assert.AreEqual("ACGT-", dnaStringActual);
Assert.AreEqual("ACGU-", rnaStringActual);
Assert.AreEqual("ACDEFGHIKLMNOPQRSTUVWY-*", proteinStringActual);
Assert.AreEqual("ACGT-MRSWYKVHDBN", dnaAmbiguousStringActual);
Assert.AreEqual("ACGU-NMRSWYKVHDB", rnaAmbiguousStringActual);
Assert.AreEqual("ACDEFGHIKLMNOPQRSTUVWY-*XZBJ", proteinAmbiguousStringActual);
}
