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 ValidateAmbiguousDnaAplhabet()
{
char[] ambiguousCharacters = new char[16] {
'A', 'M', 'R', 'S', 'W', 'Y', 'K', 'V', 'H', 'D', 'B', 'N', 'C', 'G', '-', 'T'
};
AmbiguousDnaAlphabet dnaAlphabetInstance = AmbiguousDnaAlphabet.Instance;
Assert.AreEqual((char)dnaAlphabetInstance.A, ambiguousCharacters[0]);
Assert.AreEqual((char)dnaAlphabetInstance.AC, ambiguousCharacters[1]);
Assert.AreEqual((char)dnaAlphabetInstance.ACT, ambiguousCharacters[8]);
Assert.AreEqual((char)dnaAlphabetInstance.AT, ambiguousCharacters[4]);
Assert.AreEqual((char)dnaAlphabetInstance.C, ambiguousCharacters[12]);
Assert.AreEqual((char)dnaAlphabetInstance.G, ambiguousCharacters[13]);
Assert.AreEqual((char)dnaAlphabetInstance.GA, ambiguousCharacters[2]);
Assert.AreEqual((char)dnaAlphabetInstance.Gap, ambiguousCharacters[14]);
Assert.AreEqual((char)dnaAlphabetInstance.GAT, ambiguousCharacters[9]);
Assert.AreEqual((char)dnaAlphabetInstance.GC, ambiguousCharacters[3]);
Assert.AreEqual((char)dnaAlphabetInstance.GCA, ambiguousCharacters[7]);
Assert.AreEqual((char)dnaAlphabetInstance.GT, ambiguousCharacters[6]);
Assert.AreEqual((char)dnaAlphabetInstance.GTC, ambiguousCharacters[10]);
Assert.AreEqual((char)dnaAlphabetInstance.T, ambiguousCharacters[15]);
Assert.AreEqual((char)dnaAlphabetInstance.TC, ambiguousCharacters[5]);
ApplicationLog.WriteLine(string.Concat(@"Alphabets BVT: Validation of
Ambiguous Dna characters completed successfully."));
}
public void TestDnaAlphabetTryGetBasicSymbols()
{
HashSet <byte> basicSymbols;
AmbiguousDnaAlphabet dnaAlphabet = AmbiguousDnaAlphabet.Instance;
Assert.AreEqual(true, dnaAlphabet.TryGetBasicSymbols((byte)'M', out basicSymbols));
Assert.IsTrue(basicSymbols.All(sy => (sy == (byte)'A' || sy == (byte)'C')));
}
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);
}
