void ValidateCompareSymbols(AlphabetsTypes option)
{
IAlphabet alphabetInstance = null;
byte byte1 = 0, byte2 = 0, byte3 = 0;
switch (option)
{
case AlphabetsTypes.Protein:
alphabetInstance = ProteinAlphabet.Instance;
byte1 = (byte)'A';
byte2 = (byte)'A';
byte3 = (byte)'B';
break;
case AlphabetsTypes.Rna:
alphabetInstance = RnaAlphabet.Instance;
byte1 = (byte)'U';
byte2 = (byte)'U';
byte3 = (byte)'A';
break;
case AlphabetsTypes.Dna:
alphabetInstance = DnaAlphabet.Instance;
byte1 = (byte)'T';
byte2 = (byte)'T';
byte3 = (byte)'A';
break;
}
Assert.AreEqual(byte1, byte2);
Assert.AreNotEqual(byte1, byte3);
ApplicationLog.WriteLine(string.Concat("Alphabets BVT: Validation of Comparing Symbols operation ",
option, " completed successfully."));
}
void ValidateGetAmbiguousCharacters(AlphabetsTypes option)
{
string referenceCharacters = "";
IAlphabet alphabetInstance = null;
switch (option)
{
case AlphabetsTypes.Protein:
referenceCharacters = "BZJX";
alphabetInstance = AmbiguousProteinAlphabet.Instance;
break;
case AlphabetsTypes.Rna:
alphabetInstance = AmbiguousRnaAlphabet.Instance;
referenceCharacters = "MRSWYKVHDBN";
break;
case AlphabetsTypes.Dna:
alphabetInstance = AmbiguousDnaAlphabet.Instance;
referenceCharacters = "MRSWYKVHDBN";
break;
}
HashSet <byte> ambiguousCharacters = new HashSet <byte>();
ambiguousCharacters = alphabetInstance.GetAmbiguousSymbols();
string ambiguosCharacters = new string(ambiguousCharacters.Select(a => (char)a).ToArray());
char[] refCharacters = referenceCharacters.ToCharArray();
for (int i = 0; i < ambiguosCharacters.Length; i++)
{
Assert.IsTrue(ambiguosCharacters.Contains(refCharacters[i]));
}
}
void ValidateGetValidSymbols(AlphabetsTypes option)
{
string referenceCharacters = "";
IAlphabet alphabetInstance = null;
switch (option)
{
case AlphabetsTypes.Protein:
referenceCharacters = "AaCcDdEeFfGgHhIiKkLlMmNnOoPpQqRrSsTtUuVvWwYy-*";
alphabetInstance = ProteinAlphabet.Instance;
break;
case AlphabetsTypes.Rna:
alphabetInstance = RnaAlphabet.Instance;
referenceCharacters = "AaCcGgUu-";
break;
case AlphabetsTypes.Dna:
alphabetInstance = DnaAlphabet.Instance;
referenceCharacters = "AaCcGgTt-";
break;
}
HashSet <byte> validSymbolsByte = new HashSet <byte>();
validSymbolsByte = alphabetInstance.GetValidSymbols();
string validSymbols = new string(validSymbolsByte.Select(a => (char)a).ToArray());
Assert.AreEqual(referenceCharacters, validSymbols);
ApplicationLog.WriteLine(string.Concat(
"Alphabets BVT: Validation of Alphabets operation ", option, " completed successfully."));
}
/// <summary>
/// Validate ValidateSequence method.
/// Input Data : Valid Dna/Rna/Protein Sequences.
/// Output Data : Validate Sequences for all Alphabet instances.
/// </summary>
void ValidateSequenceTypes(AlphabetsTypes option)
{
IAlphabet alphabetInstance = null;
string sequence = "";
switch (option)
{
case AlphabetsTypes.Protein:
alphabetInstance = ProteinAlphabet.Instance;
sequence = utilityObj.xmlUtil.GetTextValue(Constants.ProteinDerivedSequenceNode,
Constants.ExpectedDerivedSequence);
break;
case AlphabetsTypes.Rna:
alphabetInstance = RnaAlphabet.Instance;
sequence = utilityObj.xmlUtil.GetTextValue(Constants.RnaDerivedSequenceNode,
Constants.ExpectedDerivedSequence);
break;
case AlphabetsTypes.Dna:
alphabetInstance = DnaAlphabet.Instance;
sequence = utilityObj.xmlUtil.GetTextValue(Constants.DnaDerivedSequenceNode,
Constants.ExpectedDerivedSequence);
break;
}
Assert.IsTrue(alphabetInstance.ValidateSequence(encodingObj.GetBytes(sequence), 0, 4));
ApplicationLog.WriteLine(string.Concat(@"Alphabets BVT: Validation of
Validate Sequence method for ", option, " completed successfully."));
}
void ValidateTryGetAmbiguousSymbol(AlphabetsTypes option)
{
IAlphabet alphabetInstance = null;
HashSet <byte> basicSymbols = new HashSet <byte>();
byte ambiguousSymbol = 0, expectedAmbiguousSymbol = 0;
switch (option)
{
case AlphabetsTypes.Protein:
alphabetInstance = AmbiguousProteinAlphabet.Instance;
basicSymbols.Add((byte)'Q');
basicSymbols.Add((byte)'E');
expectedAmbiguousSymbol = (byte)'Z';
break;
case AlphabetsTypes.Rna:
alphabetInstance = AmbiguousRnaAlphabet.Instance;
basicSymbols.Add((byte)'G');
basicSymbols.Add((byte)'C');
expectedAmbiguousSymbol = (byte)'S';
break;
case AlphabetsTypes.Dna:
alphabetInstance = AmbiguousDnaAlphabet.Instance;
basicSymbols.Add((byte)'G');
basicSymbols.Add((byte)'A');
expectedAmbiguousSymbol = (byte)'R';
break;
}
Assert.IsTrue(alphabetInstance.TryGetAmbiguousSymbol(basicSymbols, out ambiguousSymbol));
Assert.AreEqual(expectedAmbiguousSymbol, ambiguousSymbol);
ApplicationLog.WriteLine(string.Concat(@"Alphabets BVT: Validation of
Try Get Ambiguous symbol for ", option, " completed successfully."));
}
void ValidateTryGetDefaultGapSymbol(AlphabetsTypes option)
{
IAlphabet alphabetInstance = null;
switch (option)
{
case AlphabetsTypes.Protein:
alphabetInstance = ProteinAlphabet.Instance;
break;
case AlphabetsTypes.Rna:
alphabetInstance = RnaAlphabet.Instance;
break;
case AlphabetsTypes.Dna:
alphabetInstance = DnaAlphabet.Instance;
break;
}
byte outputByte;
alphabetInstance.TryGetDefaultGapSymbol(out outputByte);
Assert.AreEqual('-', (char)outputByte);
ApplicationLog.WriteLine(string.Concat(@"Alphabets BVT: Validation of
Try Default gap symbol for ", option, " completed successfully."));
HashSet <byte> outputGapSymbol = new HashSet <byte>();
string outputGapString = "";
alphabetInstance.TryGetGapSymbols(out outputGapSymbol);
outputGapString = new string(outputGapSymbol.Select(a => (char)a).ToArray());
Assert.AreEqual("-", outputGapString);
ApplicationLog.WriteLine(string.Concat(@"Alphabets BVT: Validation of
Try Get gap symbol for ", option, " completed successfully."));
}
void ValidatePublicProperties(AlphabetsTypes option)
{
IAlphabet alphabetInstance = null;
int count = 0;
bool hasGaps = true, hasAmbiguity = true, hasTermination = true, isComplementSupported = true;
string name = "";
switch (option)
{
case AlphabetsTypes.Protein:
alphabetInstance = ProteinAlphabet.Instance;
count = 24;
hasAmbiguity = false;
hasGaps = true;
hasTermination = true;
isComplementSupported = false;
name = "Protein";
break;
case AlphabetsTypes.Rna:
alphabetInstance = RnaAlphabet.Instance;
count = 5;
hasAmbiguity = false;
hasGaps = true;
hasTermination = false;
isComplementSupported = true;
name = "Rna";
break;
case AlphabetsTypes.Dna:
alphabetInstance = DnaAlphabet.Instance;
count = 5;
hasAmbiguity = false;
hasGaps = true;
hasTermination = false;
isComplementSupported = true;
name = "Dna";
break;
}
Assert.AreEqual(count, alphabetInstance.Count);
ApplicationLog.WriteLine(string.Concat(@"Alphabets BVT: Validation of
Count property for ", option, " completed successfully."));
Assert.AreEqual(hasGaps, alphabetInstance.HasGaps);
ApplicationLog.WriteLine(string.Concat(@"Alphabets BVT: Validation of
HasGaps property for ", option, " completed successfully."));
Assert.AreEqual(hasAmbiguity, alphabetInstance.HasAmbiguity);
ApplicationLog.WriteLine(string.Concat(@"Alphabets BVT: Validation of
HasAmbiguity property for ", option, " completed successfully."));
Assert.AreEqual(hasTermination, alphabetInstance.HasTerminations);
ApplicationLog.WriteLine(string.Concat(@"Alphabets BVT: Validation of
HasTermination property for ", option, " completed successfully."));
Assert.AreEqual(isComplementSupported, alphabetInstance.IsComplementSupported);
ApplicationLog.WriteLine(string.Concat(@"Alphabets BVT: Validation of
IsComplementSupported property for ", option, " completed successfully."));
Assert.AreEqual(name, alphabetInstance.Name);
ApplicationLog.WriteLine(string.Concat(@"Alphabets BVT: Validation of
Name property for ", option, " completed successfully."));
}
void ValidateGetSymbolValueMap(AlphabetsTypes option)
{
IAlphabet alphabetInstance = null;
byte[] queryReference = null;
byte inputByte1 = 0, inputByte2 = 0, outputByte1 = 0, outputByte2 = 0;
switch (option)
{
case AlphabetsTypes.Protein:
alphabetInstance = ProteinAlphabet.Instance;
inputByte1 = (byte)'w';
outputByte1 = (byte)'W';
inputByte2 = (byte)'e';
outputByte2 = (byte)'E';
break;
case AlphabetsTypes.Rna:
alphabetInstance = RnaAlphabet.Instance;
inputByte1 = (byte)'a';
outputByte1 = (byte)'A';
inputByte2 = (byte)'u';
outputByte2 = (byte)'U';
break;
case AlphabetsTypes.Dna:
alphabetInstance = DnaAlphabet.Instance;
inputByte1 = (byte)'a';
outputByte1 = (byte)'A';
inputByte2 = (byte)'t';
outputByte2 = (byte)'T';
break;
}
byte output = 0;
queryReference = alphabetInstance.GetSymbolValueMap();
output = queryReference[inputByte1];
Assert.AreEqual(outputByte1, output);
output = queryReference[inputByte2];
Assert.AreEqual(outputByte2, output);
ApplicationLog.WriteLine(string.Concat(@"Alphabets BVT: Validation of
GetSymbolValueMap method for ", option, " completed successfully."));
}
void GetDefaultTerminationSymbol(AlphabetsTypes option)
{
IAlphabet alphabetInstance = null;
byte outputDefaultTerminationSymbol = 0;
HashSet <byte> outputTerminationSymbol = new HashSet <byte>();
string outputTerminationString = "";
switch (option)
{
case AlphabetsTypes.Protein:
alphabetInstance = ProteinAlphabet.Instance;
break;
case AlphabetsTypes.Rna:
alphabetInstance = RnaAlphabet.Instance;
break;
case AlphabetsTypes.Dna:
alphabetInstance = DnaAlphabet.Instance;
break;
}
if (option.Equals(AlphabetsTypes.Protein))
{
Assert.AreEqual(true, alphabetInstance.TryGetDefaultTerminationSymbol(out outputDefaultTerminationSymbol));
Assert.AreEqual(true, alphabetInstance.TryGetTerminationSymbols(out outputTerminationSymbol));
outputTerminationString = new string(outputTerminationSymbol.Select(a => (char)a).ToArray());
Assert.AreEqual('*', (char)outputDefaultTerminationSymbol);
Assert.AreEqual("*", outputTerminationString);
}
else
{
Assert.AreEqual(false, alphabetInstance.TryGetDefaultTerminationSymbol(out outputDefaultTerminationSymbol));
Assert.AreEqual(false, alphabetInstance.TryGetTerminationSymbols(out outputTerminationSymbol));
}
ApplicationLog.WriteLine(string.Concat("Alphabets BVT: Validation of Get Default termination symbol for",
option, " completed successfully."));
}
void TryGetComplementSymbol(AlphabetsTypes option)
{
IAlphabet alphabetInstance = null;
byte inputByte = 0, complementByte = 0, outputByte = 0;
switch (option)
{
case AlphabetsTypes.Protein:
alphabetInstance = ProteinAlphabet.Instance;
inputByte = (byte)'F';
complementByte = (byte)'U';
break;
case AlphabetsTypes.Rna:
alphabetInstance = RnaAlphabet.Instance;
inputByte = (byte)'A';
complementByte = (byte)'U';
break;
case AlphabetsTypes.Dna:
alphabetInstance = DnaAlphabet.Instance;
inputByte = (byte)'A';
complementByte = (byte)'T';
break;
}
if (!option.Equals(AlphabetsTypes.Protein))
{
Assert.AreEqual(true, alphabetInstance.TryGetComplementSymbol(inputByte, out outputByte));
Assert.AreEqual(complementByte, outputByte);
}
else
{
Assert.AreEqual(false, alphabetInstance.TryGetComplementSymbol(inputByte, out outputByte));
}
ApplicationLog.WriteLine(string.Concat("Alphabets BVT: Validation of Get Complement operation for",
option, " completed successfully."));
}
void ValidateTryGetBasicSymbols(AlphabetsTypes option)
{
IAlphabet alphabetInstance = null;
byte basicSymbol = 0, expectedSymbol1 = 0, expectedSymbol2 = 0;
switch (option)
{
case AlphabetsTypes.Protein:
alphabetInstance = AmbiguousProteinAlphabet.Instance;
basicSymbol = (byte)'Z';
expectedSymbol1 = (byte)'Q';
expectedSymbol2 = (byte)'E';
break;
case AlphabetsTypes.Rna:
alphabetInstance = AmbiguousRnaAlphabet.Instance;
basicSymbol = (byte)'R';
expectedSymbol1 = (byte)'G';
expectedSymbol2 = (byte)'A';
break;
case AlphabetsTypes.Dna:
basicSymbol = (byte)'M';
expectedSymbol1 = (byte)'A';
expectedSymbol2 = (byte)'C';
alphabetInstance = AmbiguousDnaAlphabet.Instance;
break;
}
HashSet <byte> basicSymbols;
Assert.AreEqual(true, alphabetInstance.TryGetBasicSymbols(basicSymbol, out basicSymbols));
Assert.IsTrue(basicSymbols.All(sy => (sy == expectedSymbol1 || sy == expectedSymbol2)));
ApplicationLog.WriteLine(string.Concat(@"Alphabets BVT: Validation of
Try Get Basics symbol for ", option, " completed successfully."));
}
void ValidateGetValidSymbols(AlphabetsTypes option)
{
string referenceCharacters = "";
IAlphabet alphabetInstance = null;
switch (option)
{
case AlphabetsTypes.Protein:
referenceCharacters = "AaCcDdEeFfGgHhIiKkLlMmNnOoPpQqRrSsTtUuVvWwYy-*";
alphabetInstance = ProteinAlphabet.Instance;
break;
case AlphabetsTypes.Rna:
alphabetInstance = RnaAlphabet.Instance;
referenceCharacters = "AaCcGgUu-";
break;
case AlphabetsTypes.Dna:
alphabetInstance = DnaAlphabet.Instance;
referenceCharacters = "AaCcGgTt-";
break;
}
HashSet<byte> validSymbolsByte = new HashSet<byte>();
validSymbolsByte = alphabetInstance.GetValidSymbols();
string validSymbols = new string(validSymbolsByte.Select(a => (char)a).ToArray());
Assert.AreEqual(referenceCharacters, validSymbols);
ApplicationLog.WriteLine(string.Concat(
"Alphabets BVT: Validation of Alphabets operation ", option, " completed successfully."));
}
void ValidateCompareSymbols(AlphabetsTypes option)
{
IAlphabet alphabetInstance = null;
byte byte1 = 0, byte2 = 0, byte3 = 0;
switch (option)
{
case AlphabetsTypes.Protein:
alphabetInstance = ProteinAlphabet.Instance;
byte1 = (byte)'A';
byte2 = (byte)'A';
byte3 = (byte)'B';
break;
case AlphabetsTypes.Rna:
alphabetInstance = RnaAlphabet.Instance;
byte1 = (byte)'U';
byte2 = (byte)'U';
byte3 = (byte)'A';
break;
case AlphabetsTypes.Dna:
alphabetInstance = DnaAlphabet.Instance;
byte1 = (byte)'T';
byte2 = (byte)'T';
byte3 = (byte)'A';
break;
}
Assert.AreEqual(byte1, byte2);
Assert.AreNotEqual(byte1, byte3);
ApplicationLog.WriteLine(string.Concat("Alphabets BVT: Validation of Comparing Symbols operation ",
option, " completed successfully."));
}
void ValidateGetSymbolValueMap(AlphabetsTypes option)
{
IAlphabet alphabetInstance = null;
byte[] queryReference = null;
byte inputByte1 = 0, inputByte2 = 0, outputByte1 = 0, outputByte2 = 0;
switch (option)
{
case AlphabetsTypes.Protein:
alphabetInstance = ProteinAlphabet.Instance;
inputByte1 = (byte)'w';
outputByte1 = (byte)'W';
inputByte2 = (byte)'e';
outputByte2 = (byte)'E';
break;
case AlphabetsTypes.Rna:
alphabetInstance = RnaAlphabet.Instance;
inputByte1 = (byte)'a';
outputByte1 = (byte)'A';
inputByte2 = (byte)'u';
outputByte2 = (byte)'U';
break;
case AlphabetsTypes.Dna:
alphabetInstance = DnaAlphabet.Instance;
inputByte1 = (byte)'a';
outputByte1 = (byte)'A';
inputByte2 = (byte)'t';
outputByte2 = (byte)'T';
break;
}
byte output = 0;
queryReference = alphabetInstance.GetSymbolValueMap();
output = queryReference[inputByte1];
Assert.AreEqual(outputByte1, output);
output = queryReference[inputByte2];
Assert.AreEqual(outputByte2, output);
ApplicationLog.WriteLine(string.Concat(@"Alphabets BVT: Validation of
GetSymbolValueMap method for ", option, " completed successfully."));
}
void ValidateGetAmbiguousCharacters(AlphabetsTypes option)
{
string referenceCharacters = "";
IAlphabet alphabetInstance = null;
switch (option)
{
case AlphabetsTypes.Protein:
referenceCharacters = "BZJX";
alphabetInstance = AmbiguousProteinAlphabet.Instance;
break;
case AlphabetsTypes.Rna:
alphabetInstance = AmbiguousRnaAlphabet.Instance;
referenceCharacters = "MRSWYKVHDBN";
break;
case AlphabetsTypes.Dna:
alphabetInstance = AmbiguousDnaAlphabet.Instance;
referenceCharacters = "MRSWYKVHDBN";
break;
}
HashSet<byte> ambiguousCharacters = new HashSet<byte>();
ambiguousCharacters = alphabetInstance.GetAmbiguousSymbols();
string ambiguosCharacters = new string(ambiguousCharacters.Select(a => (char)a).ToArray());
char[] refCharacters = referenceCharacters.ToCharArray();
for (int i = 0; i < ambiguosCharacters.Length; i++)
{
Assert.IsTrue(ambiguosCharacters.Contains(refCharacters[i]));
}
}
void ValidatePublicProperties(AlphabetsTypes option)
{
IAlphabet alphabetInstance = null;
int count = 0;
bool hasGaps = true, hasAmbiguity = true, hasTermination = true, isComplementSupported = true;
string name = "";
switch (option)
{
case AlphabetsTypes.Protein:
alphabetInstance = ProteinAlphabet.Instance;
count = 24;
hasAmbiguity = false;
hasGaps = true;
hasTermination = true;
isComplementSupported = false;
name = "Protein";
break;
case AlphabetsTypes.Rna:
alphabetInstance = RnaAlphabet.Instance;
count = 5;
hasAmbiguity = false;
hasGaps = true;
hasTermination = false;
isComplementSupported = true;
name = "Rna";
break;
case AlphabetsTypes.Dna:
alphabetInstance = DnaAlphabet.Instance;
count = 5;
hasAmbiguity = false;
hasGaps = true;
hasTermination = false;
isComplementSupported = true;
name = "Dna";
break;
}
Assert.AreEqual(count, alphabetInstance.Count);
ApplicationLog.WriteLine(string.Concat(@"Alphabets BVT: Validation of
Count property for ", option, " completed successfully."));
Assert.AreEqual(hasGaps, alphabetInstance.HasGaps);
ApplicationLog.WriteLine(string.Concat(@"Alphabets BVT: Validation of
HasGaps property for ", option, " completed successfully."));
Assert.AreEqual(hasAmbiguity, alphabetInstance.HasAmbiguity);
ApplicationLog.WriteLine(string.Concat(@"Alphabets BVT: Validation of
HasAmbiguity property for ", option, " completed successfully."));
Assert.AreEqual(hasTermination, alphabetInstance.HasTerminations);
ApplicationLog.WriteLine(string.Concat(@"Alphabets BVT: Validation of
HasTermination property for ", option, " completed successfully."));
Assert.AreEqual(isComplementSupported, alphabetInstance.IsComplementSupported);
ApplicationLog.WriteLine(string.Concat(@"Alphabets BVT: Validation of
IsComplementSupported property for ", option, " completed successfully."));
Assert.AreEqual(name, alphabetInstance.Name);
ApplicationLog.WriteLine(string.Concat(@"Alphabets BVT: Validation of
Name property for ", option, " completed successfully."));
}
/// <summary>
/// Validate ValidateSequence method.
/// Input Data : Valid Dna/Rna/Protein Sequences.
/// Output Data : Validate Sequences for all Alphabet instances.
/// </summary>
void ValidateSequenceTypes(AlphabetsTypes option)
{
IAlphabet alphabetInstance = null;
string sequence = "";
switch (option)
{
case AlphabetsTypes.Protein:
alphabetInstance = ProteinAlphabet.Instance;
sequence = this.utilityObj.xmlUtil.GetTextValue(Constants.ProteinDerivedSequenceNode,
Constants.ExpectedDerivedSequence);
break;
case AlphabetsTypes.Rna:
alphabetInstance = RnaAlphabet.Instance;
sequence = this.utilityObj.xmlUtil.GetTextValue(Constants.RnaDerivedSequenceNode,
Constants.ExpectedDerivedSequence);
break;
case AlphabetsTypes.Dna:
alphabetInstance = DnaAlphabet.Instance;
sequence = this.utilityObj.xmlUtil.GetTextValue(Constants.DnaDerivedSequenceNode,
Constants.ExpectedDerivedSequence);
break;
}
Assert.IsTrue(alphabetInstance.ValidateSequence(UTF8Encoding.UTF8.GetBytes(sequence), 0, 4));
ApplicationLog.WriteLine(string.Concat(@"Alphabets BVT: Validation of
Validate Sequence method for ", option, " completed successfully."));
}
void ValidateTryGetAmbiguousSymbol(AlphabetsTypes option)
{
IAlphabet alphabetInstance = null;
HashSet<byte> basicSymbols = new HashSet<byte>();
byte ambiguousSymbol = 0, expectedAmbiguousSymbol = 0;
switch (option)
{
case AlphabetsTypes.Protein:
alphabetInstance = AmbiguousProteinAlphabet.Instance;
basicSymbols.Add((byte)'Q');
basicSymbols.Add((byte)'E');
expectedAmbiguousSymbol = (byte)'Z';
break;
case AlphabetsTypes.Rna:
alphabetInstance = AmbiguousRnaAlphabet.Instance;
basicSymbols.Add((byte)'G');
basicSymbols.Add((byte)'C');
expectedAmbiguousSymbol = (byte)'S';
break;
case AlphabetsTypes.Dna:
alphabetInstance = AmbiguousDnaAlphabet.Instance;
basicSymbols.Add((byte)'G');
basicSymbols.Add((byte)'A');
expectedAmbiguousSymbol = (byte)'R';
break;
}
Assert.IsTrue(alphabetInstance.TryGetAmbiguousSymbol(basicSymbols, out ambiguousSymbol));
Assert.AreEqual(expectedAmbiguousSymbol, ambiguousSymbol);
ApplicationLog.WriteLine(string.Concat(@"Alphabets BVT: Validation of
Try Get Ambiguous symbol for ", option, " completed successfully."));
}
void ValidateTryGetBasicSymbols(AlphabetsTypes option)
{
IAlphabet alphabetInstance = null;
byte basicSymbol = 0, expectedSymbol1 = 0, expectedSymbol2 = 0;
switch (option)
{
case AlphabetsTypes.Protein:
alphabetInstance = AmbiguousProteinAlphabet.Instance;
basicSymbol = (byte)'Z';
expectedSymbol1 = (byte)'Q';
expectedSymbol2 = (byte)'E';
break;
case AlphabetsTypes.Rna:
alphabetInstance = AmbiguousRnaAlphabet.Instance;
basicSymbol = (byte)'R';
expectedSymbol1 = (byte)'G';
expectedSymbol2 = (byte)'A';
break;
case AlphabetsTypes.Dna:
basicSymbol = (byte)'M';
expectedSymbol1 = (byte)'A';
expectedSymbol2 = (byte)'C';
alphabetInstance = AmbiguousDnaAlphabet.Instance;
break;
}
HashSet<byte> basicSymbols;
Assert.AreEqual(true, alphabetInstance.TryGetBasicSymbols(basicSymbol, out basicSymbols));
Assert.IsTrue(basicSymbols.All(sy => (sy == expectedSymbol1 || sy == expectedSymbol2)));
ApplicationLog.WriteLine(string.Concat(@"Alphabets BVT: Validation of
Try Get Basics symbol for ", option, " completed successfully."));
}
void TryGetComplementSymbol(AlphabetsTypes option)
{
IAlphabet alphabetInstance = null;
byte inputByte = 0, complementByte = 0, outputByte = 0;
switch (option)
{
case AlphabetsTypes.Protein:
alphabetInstance = ProteinAlphabet.Instance;
inputByte = (byte)'F';
complementByte = (byte)'U';
break;
case AlphabetsTypes.Rna:
alphabetInstance = RnaAlphabet.Instance;
inputByte = (byte)'A';
complementByte = (byte)'U';
break;
case AlphabetsTypes.Dna:
alphabetInstance = DnaAlphabet.Instance;
inputByte = (byte)'A';
complementByte = (byte)'T';
break;
}
if (!option.Equals(AlphabetsTypes.Protein))
{
Assert.AreEqual(true, alphabetInstance.TryGetComplementSymbol(inputByte, out outputByte));
Assert.AreEqual(complementByte, outputByte);
}
else
{
Assert.AreEqual(false, alphabetInstance.TryGetComplementSymbol(inputByte, out outputByte));
}
ApplicationLog.WriteLine(string.Concat("Alphabets BVT: Validation of Get Complement operation for",
option, " completed successfully."));
}
void GetDefaultTerminationSymbol(AlphabetsTypes option)
{
IAlphabet alphabetInstance = null;
byte outputDefaultTerminationSymbol = 0;
HashSet<byte> outputTerminationSymbol = new HashSet<byte>();
string outputTerminationString = "";
switch (option)
{
case AlphabetsTypes.Protein:
alphabetInstance = ProteinAlphabet.Instance;
break;
case AlphabetsTypes.Rna:
alphabetInstance = RnaAlphabet.Instance;
break;
case AlphabetsTypes.Dna:
alphabetInstance = DnaAlphabet.Instance;
break;
}
if (option.Equals(AlphabetsTypes.Protein))
{
Assert.AreEqual(true, alphabetInstance.TryGetDefaultTerminationSymbol(out outputDefaultTerminationSymbol));
Assert.AreEqual(true, alphabetInstance.TryGetTerminationSymbols(out outputTerminationSymbol));
outputTerminationString = new string(outputTerminationSymbol.Select(a => (char)a).ToArray());
Assert.AreEqual('*', (char)outputDefaultTerminationSymbol);
Assert.AreEqual("*", outputTerminationString);
}
else
{
Assert.AreEqual(false, alphabetInstance.TryGetDefaultTerminationSymbol(out outputDefaultTerminationSymbol));
Assert.AreEqual(false, alphabetInstance.TryGetTerminationSymbols(out outputTerminationSymbol));
}
ApplicationLog.WriteLine(string.Concat("Alphabets BVT: Validation of Get Default termination symbol for",
option, " completed successfully."));
}
void ValidateTryGetDefaultGapSymbol(AlphabetsTypes option)
{
IAlphabet alphabetInstance = null;
switch (option)
{
case AlphabetsTypes.Protein:
alphabetInstance = ProteinAlphabet.Instance;
break;
case AlphabetsTypes.Rna:
alphabetInstance = RnaAlphabet.Instance;
break;
case AlphabetsTypes.Dna:
alphabetInstance = DnaAlphabet.Instance;
break;
}
byte outputByte;
alphabetInstance.TryGetDefaultGapSymbol(out outputByte);
Assert.AreEqual('-', (char)outputByte);
ApplicationLog.WriteLine(string.Concat(@"Alphabets BVT: Validation of
Try Default gap symbol for ", option, " completed successfully."));
HashSet<byte> outputGapSymbol = new HashSet<byte>();
string outputGapString = "";
alphabetInstance.TryGetGapSymbols(out outputGapSymbol);
outputGapString = new string(outputGapSymbol.Select(a => (char)a).ToArray());
Assert.AreEqual("-", outputGapString);
ApplicationLog.WriteLine(string.Concat(@"Alphabets BVT: Validation of
Try Get gap symbol for ", option, " completed successfully."));
}
