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 ValidateDnaAlphabetCompareSymbols()
{
DnaAlphabet alp = DnaAlphabet.Instance;
Assert.IsTrue(alp.CompareSymbols(65, 65));
ApplicationLog.WriteLine(
"Alphabets BVT: Validation of CompareSymbols() method completed successfully.");
Console.WriteLine(
"Alphabets BVT: Validation of CompareSymbols() method completed successfully.");
}
public void ValidateDnaAlphabetLookupAll()
{
DnaAlphabet alp = DnaAlphabet.Instance;
List <ISequenceItem> itm = alp.LookupAll(true, true, true, true);
Assert.AreEqual(15, itm.Count);
// Logs to the NUnit GUI window
ApplicationLog.WriteLine(
"Alphabets BVT: Validation of LookupAll() method completed successfully.");
Console.WriteLine(
"Alphabets BVT: Validation of LookupAll() method completed successfully.");
}
public void ValidateDnaAlphabetLookupBySymbol()
{
DnaAlphabet alp = DnaAlphabet.Instance;
ISequenceItem itm = alp.LookupBySymbol("A");
Assert.AreEqual('A', itm.Symbol);
// Logs to the NUnit GUI window
ApplicationLog.WriteLine(
"Alphabets BVT: Validation of LookupBySymbol() method completed successfully.");
Console.WriteLine(
"Alphabets BVT: Validation of LookupBySymbol() method completed successfully.");
}
public void ValidateDnaAlphabetCopyTo()
{
ISequence seq = new Sequence(Alphabets.DNA, "AAAAAAAAAAAAAAAA");
DnaAlphabet alp = DnaAlphabet.Instance;
ISequenceItem[] item = seq.ToArray();
alp.CopyTo(item, 0);
Assert.AreEqual('A', item[0].Symbol);
// Logs to the NUnit GUI window
ApplicationLog.WriteLine(
"Alphabets BVT: Validation of CopyTo() method completed successfully.");
Console.WriteLine(
"Alphabets BVT: Validation of CopyTo() method completed successfully.");
}
public void ValidateDnaAlphabetClear()
{
DnaAlphabet alp = DnaAlphabet.Instance;
try
{
alp.Clear();
Assert.Fail();
}
catch (Exception)
{
// Logs to the NUnit GUI window
ApplicationLog.WriteLine("Alphabets BVT: Validation of Clear() method completed successfully.");
Console.WriteLine("Alphabets BVT: Validation of Clear() method completed successfully.");
}
}
public void InValidateDnaAlphabetRemove()
{
try
{
DnaAlphabet alp = DnaAlphabet.Instance;
alp.Remove(null as ISequenceItem);
Assert.Fail();
}
catch (Exception)
{
// Logs to the NUnit GUI window
ApplicationLog.WriteLine(
"Alphabets P2: Validation of Remove() method completed successfully.");
Console.WriteLine(
"Alphabets P2: Validation of Remove() method completed successfully.");
}
}
public void InValidateDnaAlphabetGetBasicSymbols()
{
DnaAlphabet alp = DnaAlphabet.Instance;
try
{
alp.GetBasicSymbols(null);
Assert.Fail();
}
catch (ArgumentException)
{
// Logs to the NUnit GUI window
ApplicationLog.WriteLine(
"Alphabets P2: Validation of GetBasicSymbols() method completed successfully.");
Console.WriteLine(
"Alphabets P2: Validation of GetBasicSymbols() method completed successfully.");
}
}
public void ValidateDnaAlphabetAllProperties()
{
DnaAlphabet alp = DnaAlphabet.Instance;
Assert.AreEqual(16, alp.Count);
Assert.AreEqual('-', alp.DefaultGap.Symbol);
Assert.IsTrue(alp.HasAmbiguity);
Assert.IsTrue(alp.HasGaps);
Assert.IsFalse(alp.HasTerminations);
Assert.IsTrue(alp.IsReadOnly);
Assert.AreEqual("DNA", alp.Name);
// Logs to the NUnit GUI window
ApplicationLog.WriteLine(
"Alphabets BVT: Validation of All properties completed successfully.");
Console.WriteLine(
"Alphabets BVT: Validation of All properties method completed successfully.");
}
public void InValidateDnaAlphabetLookupBySymbol()
{
DnaAlphabet alp = DnaAlphabet.Instance;
try
{
ISequenceItem itm = alp.LookupBySymbol("");
Assert.IsNotNull(itm);
Assert.Fail();
}
catch (ArgumentException)
{
// Logs to the NUnit GUI window
ApplicationLog.WriteLine(
"Alphabets P2: Validation of LookupBySymbol() method completed successfully.");
Console.WriteLine(
"Alphabets P2: Validation of LookupBySymbol() method completed successfully.");
}
}
public void ValidateDnaAlphabetGetConsensusSymbol()
{
ISequence seq = new Sequence(Alphabets.DNA, "ATGCA");
DnaAlphabet alp = DnaAlphabet.Instance;
HashSet <ISequenceItem> hashSet = new HashSet <ISequenceItem>();
foreach (ISequenceItem item in seq)
{
hashSet.Add(item);
}
Assert.IsNotNull(alp.GetConsensusSymbol(hashSet));
// Logs to the NUnit GUI window
ApplicationLog.WriteLine(
"Alphabets BVT: Validation of GetBasicSymbols() method completed successfully.");
Console.WriteLine(
"Alphabets BVT: Validation of GetBasicSymbols() method completed successfully.");
}
public void ValidateDnaAlphabetGetBasicSymbols()
{
ISequence seq = new Sequence(Alphabets.DNA, "AGCTB");
DnaAlphabet alp = DnaAlphabet.Instance;
ISequenceItem item = seq[4];
Assert.IsNotNull(alp.GetBasicSymbols(item));
item = seq[3];
Assert.IsNotNull(alp.GetBasicSymbols(item));
item = seq[3];
Assert.IsNotNull(alp.GetBasicSymbols(item));
// Logs to the NUnit GUI window
ApplicationLog.WriteLine(
"Alphabets BVT: Validation of GetBasicSymbols() method completed successfully.");
Console.WriteLine(
"Alphabets BVT: Validation of GetBasicSymbols() method completed successfully.");
}
public void TestDnaAlphabetTryGetComplementSymbol()
{
byte basicSymbols;
DnaAlphabet dnaAlphabet = DnaAlphabet.Instance;
Assert.AreEqual(true, dnaAlphabet.TryGetComplementSymbol((byte)'A', out basicSymbols));
Assert.AreEqual('T', (char)basicSymbols);
Assert.AreEqual(true, dnaAlphabet.TryGetComplementSymbol((byte)'T', out basicSymbols));
Assert.AreEqual('A', (char)basicSymbols);
Assert.AreEqual(true, dnaAlphabet.TryGetComplementSymbol((byte)'G', out basicSymbols));
Assert.AreEqual('C', (char)basicSymbols);
Assert.AreEqual(true, dnaAlphabet.TryGetComplementSymbol((byte)'C', out basicSymbols));
Assert.AreEqual('G', (char)basicSymbols);
Assert.AreEqual('G', (char)dnaAlphabet.GetSymbolValueMap()[(byte)'g']);
Assert.IsTrue(dnaAlphabet.CompareSymbols((byte)'T', (byte)'t'));
Assert.IsTrue(dnaAlphabet.CompareSymbols((byte)'t', (byte)'T'));
Assert.AreEqual(dnaAlphabet.GetAmbiguousSymbols().Count, 0);
}
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);
}
public void ValidateDnaAlphabetAdd()
{
// Gets the actual sequence and the alphabet from the Xml
string alphabetName = Utility._xmlUtil.GetTextValue(Constants.SimpleDnaAlphabetNode,
Constants.AlphabetNameNode);
string actualSequence = Utility._xmlUtil.GetTextValue(Constants.SimpleDnaAlphabetNode,
Constants.ExpectedSingleChar);
ISequence seq = new Sequence(Utility.GetAlphabet(alphabetName), actualSequence);
DnaAlphabet alp = DnaAlphabet.Instance;
try
{
alp.Add(seq[0]);
Assert.Fail();
}
catch (Exception)
{
// Logs to the NUnit GUI window
ApplicationLog.WriteLine("Alphabets BVT: Validation of Add() method completed successfully.");
Console.WriteLine("Alphabets BVT: Validation of Add() method completed successfully.");
}
}
private void InitializeAlignment()
{
DnaAlphabet dna = DnaAlphabet.Instance;
}
