private void InValidateSmithWatermanAlignmentWithInvalidSimilarityMatrix(string nodeName,
bool isTextFile,
SimilarityMatrixInvalidTypes
invalidType,
AlignParameters additionalParameter,
AlignmentType alignType)
{
Sequence aInput = null;
Sequence bInput = null;
ISequence inputSequence1;
ISequence inputSequence2;
IAlphabet alphabet = Utility.GetAlphabet(this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.AlphabetNameNode));
if (isTextFile)
{
// Read the xml file for getting both the files for aligning.
string firstInputFilepath = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode1);
string secondInputFilepath = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode2);
// Parse the files and get the sequence.
var parseObjectForFile1 = new FastAParser { Alphabet = alphabet };
inputSequence1 = parseObjectForFile1.Parse(firstInputFilepath).ElementAt(0);
inputSequence2 = parseObjectForFile1.Parse(secondInputFilepath).ElementAt(0);
// Create input sequence for sequence string in different cases.
GetSequenceWithCaseType(new string(inputSequence1.Select(a => (char) a).ToArray()),
new string(inputSequence2.Select(a => (char) a).ToArray()),
alphabet, SequenceCaseType.LowerCase, out aInput, out bInput);
}
else
{
string firstInputSequence = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceNode1);
string secondInputSequence = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceNode2);
// Create input sequence for sequence string in different cases.
GetSequenceWithCaseType(firstInputSequence, secondInputSequence,
alphabet, SequenceCaseType.LowerCase, out aInput, out bInput);
}
ApplicationLog.WriteLine(string.Concat(
"SmithWatermanAligner P2 : First sequence used is '{0}'.",
new string(aInput.Select(a => (char) a).ToArray())));
ApplicationLog.WriteLine(string.Concat(
"SmithWatermanAligner P2 : Second sequence used is '{0}'.",
new string(bInput.Select(a => (char) a).ToArray())));
// Create similarity matrix object for a invalid file.
string blosumFilePath = this.GetSimilarityMatrixFileWithInvalidType(nodeName, invalidType);
Exception actualExpection = null;
// For invalid similarity matrix data format; exception will be thrown while instantiating
SimilarityMatrix sm = null;
try
{
if (invalidType != SimilarityMatrixInvalidTypes.NullSimilarityMatrix)
{
sm = new SimilarityMatrix(new StreamReader(blosumFilePath));
}
}
catch (InvalidDataException ex)
{
actualExpection = ex;
}
// For non matching similarity matrix exception will be thrown while alignment
if (actualExpection == null)
{
int gapOpenCost = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.GapOpenCostNode), null);
int gapExtensionCost = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.GapExtensionCostNode), null);
// Create SmithWatermanAligner instance and set its values.
var smithWatermanObj = new SmithWatermanAligner();
if (additionalParameter != AlignParameters.AllParam)
{
smithWatermanObj.SimilarityMatrix = sm;
smithWatermanObj.GapOpenCost = gapOpenCost;
smithWatermanObj.GapExtensionCost = gapExtensionCost;
}
// Align the input sequences and catch the exception.
switch (additionalParameter)
{
case AlignParameters.AlignList:
switch (alignType)
{
case AlignmentType.Align:
try
{
smithWatermanObj.Align(new List<ISequence> {aInput, bInput});
}
catch (ArgumentException ex)
{
actualExpection = ex;
}
break;
default:
try
{
smithWatermanObj.AlignSimple(new List<ISequence> {aInput, bInput});
}
catch (ArgumentException ex)
{
actualExpection = ex;
}
break;
}
break;
case AlignParameters.AlignTwo:
switch (alignType)
{
case AlignmentType.Align:
try
{
smithWatermanObj.Align(aInput, bInput);
}
catch (ArgumentException ex)
{
actualExpection = ex;
}
break;
default:
try
{
smithWatermanObj.AlignSimple(aInput, bInput);
}
catch (ArgumentException ex)
{
actualExpection = ex;
}
break;
}
break;
case AlignParameters.AllParam:
switch (alignType)
{
case AlignmentType.Align:
try
{
smithWatermanObj.Align(sm, gapOpenCost, gapExtensionCost,
aInput, bInput);
}
catch (ArgumentException ex)
{
actualExpection = ex;
}
break;
default:
try
{
smithWatermanObj.AlignSimple(sm, gapOpenCost, aInput, bInput);
}
catch (ArgumentException ex)
{
actualExpection = ex;
}
break;
}
break;
default:
break;
}
}
// Validate that expected exception is thrown using error message.
string expectedErrorMessage = this.GetExpectedErrorMeesageWithInvalidSimilarityMatrixType(nodeName,
invalidType);
Assert.AreEqual(expectedErrorMessage, actualExpection.Message);
ApplicationLog.WriteLine(string.Concat(
"SmithWatermanAligner P2 : Expected Error message is thrown ", expectedErrorMessage));
}
private void ValidateSmithWatermanAlignment(string nodeName, bool isTextFile,
SequenceCaseType caseType, AlignParameters additionalParameter,
AlignmentType alignType,
SimilarityMatrixParameters similarityMatrixParam)
{
Sequence aInput, bInput;
IAlphabet alphabet =
Utility.GetAlphabet(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.AlphabetNameNode));
if (isTextFile)
{
// Read the xml file for getting both the files for aligning.
string filePath1 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode1);
string filePath2 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode2);
// Parse the files and get the sequence.
ISequence originalSequence1 = null;
ISequence originalSequence2 = null;
var parseObjectForFile1 = new FastAParser { Alphabet = alphabet };
originalSequence1 = parseObjectForFile1.Parse(filePath1).ElementAt(0);
originalSequence2 = parseObjectForFile1.Parse(filePath2).ElementAt(0);
// Create input sequence for sequence string in different cases.
GetSequenceWithCaseType(originalSequence1.ConvertToString(), originalSequence2.ConvertToString(),
alphabet, caseType, out aInput, out bInput);
}
else
{
string originalSequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceNode1);
string originalSequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceNode2);
// Create input sequence for sequence string in different cases.
GetSequenceWithCaseType(
originalSequence1,
originalSequence2,
alphabet,
caseType,
out aInput,
out bInput);
}
ApplicationLog.WriteLine(string.Format("SmithWatermanAligner P2 : First sequence used is '{0}'.",
aInput.ConvertToString()));
ApplicationLog.WriteLine(string.Format("SmithWatermanAligner P2 : Second sequence used is '{0}'.",
bInput.ConvertToString()));
// Create similarity matrix object for a given file.
string blosumFilePath = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.BlosumFilePathNode);
SimilarityMatrix sm;
switch (similarityMatrixParam)
{
case SimilarityMatrixParameters.TextReader:
using (TextReader reader = new StreamReader(blosumFilePath))
sm = new SimilarityMatrix(reader);
break;
case SimilarityMatrixParameters.DiagonalMatrix:
string matchValue = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MatchScoreNode);
string misMatchValue = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.MisMatchScoreNode);
sm = new DiagonalSimilarityMatrix(int.Parse(matchValue, null),
int.Parse(misMatchValue, null));
break;
default:
sm = new SimilarityMatrix(new StreamReader(blosumFilePath));
break;
}
int gapOpenCost = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.GapOpenCostNode), null);
int gapExtensionCost = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.GapExtensionCostNode),
null);
// Create SmithWatermanAligner instance and set its values.
var smithWatermanObj = new SmithWatermanAligner();
if (additionalParameter != AlignParameters.AllParam)
{
smithWatermanObj.SimilarityMatrix = sm;
smithWatermanObj.GapOpenCost = gapOpenCost;
smithWatermanObj.GapExtensionCost = gapExtensionCost;
}
IList<IPairwiseSequenceAlignment> result = null;
// Align the input sequences.
switch (additionalParameter)
{
case AlignParameters.AlignList:
switch (alignType)
{
case AlignmentType.Align:
result = smithWatermanObj.Align(new List<ISequence> {aInput, bInput});
break;
default:
result = smithWatermanObj.AlignSimple(new List<ISequence> {aInput, bInput});
break;
}
break;
case AlignParameters.AlignTwo:
switch (alignType)
{
case AlignmentType.Align:
result = smithWatermanObj.Align(aInput, bInput);
break;
default:
result = smithWatermanObj.AlignSimple(aInput, bInput);
break;
}
break;
case AlignParameters.AllParam:
switch (alignType)
{
case AlignmentType.Align:
result = smithWatermanObj.Align(sm, gapOpenCost,
gapExtensionCost, aInput, bInput);
break;
default:
result = smithWatermanObj.AlignSimple(sm, gapOpenCost, aInput, bInput);
break;
}
break;
default:
break;
}
// Get the expected sequence and scorde from xml config.
string expectedSequence1, expectedSequence2, expectedScore;
switch (alignType)
{
case AlignmentType.Align:
expectedScore = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedGapExtensionScoreNode);
switch (caseType)
{
case SequenceCaseType.LowerCase:
expectedSequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants
.ExpectedGapExtensionSequence1InLower);
expectedSequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants
.ExpectedGapExtensionSequence2InLower);
break;
default:
expectedSequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants
.ExpectedGapExtensionSequence1Node);
expectedSequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants
.ExpectedGapExtensionSequence2Node);
break;
}
break;
default:
expectedScore = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedScoreNode);
switch (caseType)
{
case SequenceCaseType.LowerCase:
expectedSequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedSequence1inLowerNode);
expectedSequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedSequence2inLowerNode);
break;
case SequenceCaseType.LowerUpperCase:
expectedSequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedSequence1inLowerNode);
expectedSequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedSequenceNode2);
break;
default:
expectedSequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedSequenceNode1);
expectedSequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedSequenceNode2);
break;
}
break;
}
// Match the alignment result with expected result.
IList<IPairwiseSequenceAlignment> expectedOutput = new List<IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment align = new PairwiseSequenceAlignment();
var alignedSeq = new PairwiseAlignedSequence
{
FirstSequence = new Sequence(alphabet, expectedSequence1),
SecondSequence = new Sequence(alphabet, expectedSequence2),
Score = Convert.ToInt32(expectedScore, null),
FirstOffset = Int32.MinValue,
SecondOffset = Int32.MinValue,
};
align.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(align);
ApplicationLog.WriteLine(string.Format(null, "SmithWatermanAligner P2 : Final Score '{0}'.", expectedScore));
ApplicationLog.WriteLine(string.Format(null, "SmithWatermanAligner P2 : Aligned First Sequence is '{0}'.",
expectedSequence1));
ApplicationLog.WriteLine(string.Format(null, "SmithWatermanAligner P2 : Aligned Second Sequence is '{0}'.",
expectedSequence2));
Assert.IsTrue(CompareAlignment(result, expectedOutput));
}
private void InValidateSmithWatermanAlignmentWithInvalidSequence(string nodeName,
bool isTextFile,
InvalidSequenceType invalidSequenceType,
AlignParameters additionalParameter,
AlignmentType alignType,
InvalidSequenceType sequenceType)
{
IAlphabet alphabet = Utility.GetAlphabet(this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.AlphabetNameNode));
Exception actualException = null;
Sequence aInput = null;
Sequence bInput = null;
if (isTextFile)
{
// Read the xml file for getting both the files for aligning.
string filepath = this.GetInputFileNameWithInvalidType(nodeName, invalidSequenceType);
// Create input sequence for sequence string in different cases.
try
{
// Parse the files and get the sequence.
IEnumerable<ISequence> seqs = null;
var parser = new FastAParser();
seqs = parser.Parse(filepath);
aInput = new Sequence(alphabet, new string(seqs.ElementAt(0).Select(a => (char) a).ToArray()));
}
catch (Exception ex)
{
actualException = ex;
}
}
else
{
string originalSequence = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.InvalidSequence1);
// Create input sequence for sequence string in different cases.
try
{
aInput = new Sequence(alphabet, originalSequence);
}
catch (ArgumentException ex)
{
actualException = ex;
}
}
if (actualException == null)
{
bInput = aInput;
// Create similarity matrix object for a given file.
string blosumFilePath = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.BlosumFilePathNode);
var sm = new SimilarityMatrix(new StreamReader(blosumFilePath));
int gapOpenCost = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.GapOpenCostNode), null);
int gapExtensionCost = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.GapExtensionCostNode), null);
// Create SmithWatermanAligner instance and set its values.
var smithWatermanObj = new SmithWatermanAligner();
if (additionalParameter != AlignParameters.AllParam)
{
smithWatermanObj.SimilarityMatrix = sm;
smithWatermanObj.GapOpenCost = gapOpenCost;
smithWatermanObj.GapExtensionCost = gapExtensionCost;
}
// Align the input sequences and catch the exception.
switch (additionalParameter)
{
case AlignParameters.AlignList:
switch (alignType)
{
case AlignmentType.Align:
try
{
smithWatermanObj.Align(new List<ISequence> {aInput, bInput});
}
catch (ArgumentException ex)
{
actualException = ex;
}
break;
default:
try
{
smithWatermanObj.AlignSimple(new List<ISequence> {aInput, bInput});
}
catch (ArgumentException ex)
{
actualException = ex;
}
break;
}
break;
case AlignParameters.AlignTwo:
switch (alignType)
{
case AlignmentType.Align:
try
{
smithWatermanObj.Align(aInput, bInput);
}
catch (ArgumentException ex)
{
actualException = ex;
}
break;
default:
try
{
smithWatermanObj.AlignSimple(aInput, bInput);
}
catch (ArgumentException ex)
{
actualException = ex;
}
break;
}
break;
case AlignParameters.AllParam:
switch (alignType)
{
case AlignmentType.Align:
try
{
smithWatermanObj.Align(sm, gapOpenCost,
gapExtensionCost, aInput, bInput);
}
catch (ArgumentException ex)
{
actualException = ex;
}
break;
default:
try
{
smithWatermanObj.AlignSimple(sm, gapOpenCost,
aInput, bInput);
}
catch (ArgumentException ex)
{
actualException = ex;
}
break;
}
break;
default:
break;
}
}
// Validate Error messages for Invalid Sequence types.
string expectedErrorMessage = this.GetExpectedErrorMeesageWithInvalidSequenceType(nodeName,
sequenceType);
Assert.AreEqual(expectedErrorMessage, actualException.Message);
ApplicationLog.WriteLine(string.Concat(
"SmithWatermanAligner P2 : Expected Error message is thrown ", expectedErrorMessage));
}
/// <summary>
/// Validates SmithWatermanAlignment algorithm for the parameters passed.
/// </summary>
/// <param name="nodeName">Xml node name</param>
/// <param name="isTextFile">Is text file an input.</param>
/// <param name="caseType">Case Type</param>
/// <param name="additionalParameter">parameter based on which certain validations are done.</param>
private void ValidateSmithWatermanAlignment(string nodeName,
bool isTextFile, SequenceCaseType caseType,
AlignParameters additionalParameter)
{
this.ValidateSmithWatermanAlignment(nodeName, isTextFile, caseType, additionalParameter,
AlignmentType.SimpleAlign);
}
/// <summary>
/// Validates SmithWatermanAlignment algorithm for the parameters passed.
/// </summary>
/// <param name="nodeName">Xml node name</param>
/// <param name="isTextFile">Is text file an input.</param>
/// <param name="caseType">Case Type</param>
/// <param name="additionalParameter">parameter based on which certain validations are done.</param>
/// <param name="alignType">Is the Align type Simple or Align with Gap Extension cost?</param>
private void ValidateSmithWatermanAlignment(string nodeName, bool isTextFile,
SequenceCaseType caseType, AlignParameters additionalParameter,
AlignmentType alignType)
{
this.ValidateSmithWatermanAlignment(nodeName, isTextFile, caseType, additionalParameter,
alignType, SimilarityMatrixParameters.Default);
}
/// <summary>
/// Validates PairwiseOverlapAlignment algorithm for the parameters passed.
/// </summary>
/// <param name="nodeName">Node Name in the xml.</param>
/// <param name="alignParam">parameter based on which certain validations are done.</param>
/// <param name="similarityMatrixParam">Similarity Matrix Parameter.</param>
private void ValidatePairwiseOverlapAlignment(string nodeName, AlignParameters alignParam,
SimilarityMatrixParameters similarityMatrixParam)
{
this.ValidatePairwiseOverlapAlignment(nodeName, alignParam,
similarityMatrixParam, AlignmentType.SimpleAlign);
}
/// <summary>
/// Validates PairwiseOverlapAlignment algorithm for the parameters passed.
/// </summary>
/// <param name="nodeName">Node Name in the xml.</param>
/// <param name="alignParam">parameter based on which certain validations are done.</param>
/// <param name="similarityMatrixParam">Similarity Matrix Parameter.</param>
/// <param name="alignType">Alignment Type</param>
private void ValidatePairwiseOverlapAlignment(string nodeName, AlignParameters alignParam,
SimilarityMatrixParameters similarityMatrixParam,
AlignmentType alignType)
{
ISequence aInput;
ISequence bInput;
IAlphabet alphabet = Utility.GetAlphabet(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.AlphabetNameNode));
if (alignParam.ToString().Contains("Code"))
{
string sequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceNode1);
string sequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceNode2);
aInput = new Sequence(alphabet, sequence1);
bInput = new Sequence(alphabet, sequence2);
}
else
{
// Read the xml file for getting both the files for aligning.
string filePath1 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode1);
string filePath2 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode2);
var parser1 = new FastAParser { Alphabet = alphabet };
aInput = parser1.Parse(filePath1).ElementAt(0);
bInput = parser1.Parse(filePath2).ElementAt(0);
}
string blosumFilePath = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.BlosumFilePathNode);
SimilarityMatrix sm;
switch (similarityMatrixParam)
{
case SimilarityMatrixParameters.TextReader:
using (TextReader reader = new StreamReader(blosumFilePath))
sm = new SimilarityMatrix(reader);
break;
case SimilarityMatrixParameters.DiagonalMatrix:
string matchValue = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MatchScoreNode);
string misMatchValue = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MisMatchScoreNode);
sm = new DiagonalSimilarityMatrix(int.Parse(matchValue, null), int.Parse(misMatchValue, null));
break;
default:
sm = new SimilarityMatrix(new StreamReader(blosumFilePath));
break;
}
int gapOpenCost = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.GapOpenCostNode), null);
int gapExtensionCost = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.GapExtensionCostNode), null);
var pairwiseOverlapObj = new PairwiseOverlapAligner();
if (AlignParameters.AllParam != alignParam)
{
pairwiseOverlapObj.SimilarityMatrix = sm;
pairwiseOverlapObj.GapOpenCost = gapOpenCost;
}
IList<IPairwiseSequenceAlignment> result = null;
switch (alignParam)
{
case AlignParameters.AlignList:
case AlignParameters.AlignListCode:
var sequences = new List<ISequence> {aInput, bInput};
switch (alignType)
{
case AlignmentType.Align:
pairwiseOverlapObj.GapExtensionCost = gapExtensionCost;
result = pairwiseOverlapObj.Align(sequences);
break;
default:
result = pairwiseOverlapObj.AlignSimple(sequences);
break;
}
break;
case AlignParameters.AllParam:
case AlignParameters.AllParamCode:
switch (alignType)
{
case AlignmentType.Align:
pairwiseOverlapObj.GapExtensionCost = gapExtensionCost;
result = pairwiseOverlapObj.Align(sm, gapOpenCost, gapExtensionCost, aInput, bInput);
break;
default:
result = pairwiseOverlapObj.AlignSimple(sm, gapOpenCost, aInput, bInput);
break;
}
break;
case AlignParameters.AlignTwo:
case AlignParameters.AlignTwoCode:
switch (alignType)
{
case AlignmentType.Align:
pairwiseOverlapObj.GapExtensionCost = gapExtensionCost;
result = pairwiseOverlapObj.Align(aInput, bInput);
break;
default:
result = pairwiseOverlapObj.AlignSimple(aInput, bInput);
break;
}
break;
default:
break;
}
// Read the xml file for getting both the files for aligning.
string expectedSequence1;
string expectedSequence2;
string expectedScore;
switch (alignType)
{
case AlignmentType.Align:
expectedScore = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedGapExtensionScoreNode);
expectedSequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedGapExtensionSequence1Node);
expectedSequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedGapExtensionSequence2Node);
break;
default:
expectedScore = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedScoreNode);
expectedSequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequenceNode1);
expectedSequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequenceNode2);
break;
}
IList<IPairwiseSequenceAlignment> expectedOutput = new List<IPairwiseSequenceAlignment>();
var seperators = new [] {';'};
string[] expectedSequences1 = expectedSequence1.Split(seperators);
string[] expectedSequences2 = expectedSequence2.Split(seperators);
IPairwiseSequenceAlignment align = new PairwiseSequenceAlignment();
for (int i = 0; i < expectedSequences1.Length; i++)
{
PairwiseAlignedSequence alignedSeq = new PairwiseAlignedSequence
{
FirstSequence = new Sequence(alphabet, expectedSequences1[i]),
SecondSequence = new Sequence(alphabet, expectedSequences2[i]),
Score = Convert.ToInt32(expectedScore, null),
FirstOffset = Int32.MinValue,
SecondOffset = Int32.MinValue,
};
align.PairwiseAlignedSequences.Add(alignedSeq);
}
expectedOutput.Add(align);
Assert.IsTrue(AlignmentHelpers.CompareAlignment(result, expectedOutput, true));
ApplicationLog.WriteLine(string.Format(null, "PairwiseOverlapAligner P1 : Final Score '{0}'.", expectedScore));
ApplicationLog.WriteLine(string.Format(null, "PairwiseOverlapAligner P1 : Aligned First Sequence is '{0}'.", expectedSequence1));
ApplicationLog.WriteLine(string.Format(null, "PairwiseOverlapAligner P1 : Aligned Second Sequence is '{0}'.", expectedSequence2));
}
/// <summary>
/// Validates PairwiseOverlapAlignment algorithm for the parameters passed.
/// </summary>
/// <param name="nodeName">Xml node name</param>
/// <param name="isTextFile">Is text file an input.</param>
/// <param name="caseType">Case Type</param>
/// <param name="additionalParameter">parameter based on which certain validations are done.</param>
/// <param name="alignType">Is the Align type Simple or Align with Gap Extension cost?</param>
/// <param name="similarityMatrixParam">Similarity Matrix</param>
private void ValidatePairwiseOverlapAlignment(string nodeName, bool isTextFile,
SequenceCaseType caseType, AlignParameters additionalParameter,
AlignmentType alignType,
SimilarityMatrixParameters similarityMatrixParam)
{
Sequence aInput = null;
Sequence bInput = null;
IAlphabet alphabet = Utility.GetAlphabet(this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.AlphabetNameNode));
if (isTextFile)
{
// Read the xml file for getting both the files for aligning.
string filePath1 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode1);
string filePath2 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode2);
var parser1 = new FastAParser();
ISequence originalSequence1 = parser1.Parse(filePath1).ElementAt(0);
ISequence originalSequence2 = parser1.Parse(filePath2).ElementAt(0);
// Create input sequence for sequence string in different cases.
GetSequenceWithCaseType(new string(originalSequence1.Select(a => (char) a).ToArray()),
new string(originalSequence2.Select(a => (char) a).ToArray()), alphabet,
caseType, out aInput, out bInput);
}
else
{
string originalSequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceNode1);
string originalSequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceNode2);
// Create input sequence for sequence string in different cases.
GetSequenceWithCaseType(
originalSequence1,
originalSequence2,
alphabet,
caseType,
out aInput,
out bInput);
}
var aInputString = new string(aInput.Select(a => (char) a).ToArray());
var bInputString = new string(bInput.Select(a => (char) a).ToArray());
ApplicationLog.WriteLine(string.Format(null,
"PairwiseOverlapAligner P2 : First sequence used is '{0}'.",
aInputString));
ApplicationLog.WriteLine(string.Format(null,
"PairwiseOverlapAligner P2 : Second sequence used is '{0}'.",
bInputString));
// Create similarity matrix object for a given file.
string blosumFilePath = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.BlosumFilePathNode);
SimilarityMatrix sm = null;
switch (similarityMatrixParam)
{
case SimilarityMatrixParameters.TextReader:
using (TextReader reader = new StreamReader(blosumFilePath))
sm = new SimilarityMatrix(reader);
break;
case SimilarityMatrixParameters.DiagonalMatrix:
string matchValue = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.MatchScoreNode);
string misMatchValue = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.MisMatchScoreNode);
sm = new DiagonalSimilarityMatrix(int.Parse(matchValue, null),
int.Parse(misMatchValue, null));
break;
default:
sm = new SimilarityMatrix(new StreamReader(blosumFilePath));
break;
}
int gapOpenCost = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.GapOpenCostNode), null);
int gapExtensionCost = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.GapExtensionCostNode), null);
// Create PairwiseOverlapAligner instance and set its values.
var pairwiseOverlapObj = new PairwiseOverlapAligner();
if (additionalParameter != AlignParameters.AllParam)
{
pairwiseOverlapObj.SimilarityMatrix = sm;
pairwiseOverlapObj.GapOpenCost = gapOpenCost;
pairwiseOverlapObj.GapExtensionCost = gapExtensionCost;
}
IList<IPairwiseSequenceAlignment> result = null;
// Align the input sequences.
switch (additionalParameter)
{
case AlignParameters.AlignList:
var sequences = new List<ISequence>();
sequences.Add(aInput);
sequences.Add(bInput);
switch (alignType)
{
case AlignmentType.Align:
result = pairwiseOverlapObj.Align(sequences);
break;
default:
result = pairwiseOverlapObj.AlignSimple(sequences);
break;
}
break;
case AlignParameters.AlignTwo:
switch (alignType)
{
case AlignmentType.Align:
result = pairwiseOverlapObj.Align(aInput, bInput);
break;
default:
result = pairwiseOverlapObj.AlignSimple(aInput, bInput);
break;
}
break;
case AlignParameters.AllParam:
switch (alignType)
{
case AlignmentType.Align:
result = pairwiseOverlapObj.Align(sm, gapOpenCost,
gapExtensionCost, aInput, bInput);
break;
default:
result = pairwiseOverlapObj.AlignSimple(sm, gapOpenCost, aInput, bInput);
break;
}
break;
default:
break;
}
aInput = null;
bInput = null;
sm = null;
// Get the expected sequence and scorde from xml config.
string expectedSequence1 = string.Empty;
string expectedSequence2 = string.Empty;
string expectedScore = string.Empty;
switch (alignType)
{
case AlignmentType.Align:
expectedScore = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedGapExtensionScoreNode);
expectedSequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedGapExtensionSequence1Node);
expectedSequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedGapExtensionSequence2Node);
break;
default:
expectedScore = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedScoreNode);
expectedSequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedSequenceNode1);
expectedSequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedSequenceNode2);
break;
}
IList<IPairwiseSequenceAlignment> expectedOutput = new List<IPairwiseSequenceAlignment>();
string[] expectedSequences1, expectedSequences2;
var seperators = new char[1] {';'};
expectedSequences1 = expectedSequence1.Split(seperators);
expectedSequences2 = expectedSequence2.Split(seperators);
IPairwiseSequenceAlignment align = new PairwiseSequenceAlignment();
PairwiseAlignedSequence alignedSeq;
for (int i = 0; i < expectedSequences1.Length; i++)
{
alignedSeq = new PairwiseAlignedSequence
{
FirstSequence = new Sequence(alphabet, expectedSequences1[i]),
SecondSequence = new Sequence(alphabet, expectedSequences2[i]),
Score = Convert.ToInt32(expectedScore, null),
FirstOffset = Int32.MinValue,
SecondOffset = Int32.MinValue,
};
align.PairwiseAlignedSequences.Add(alignedSeq);
}
expectedOutput.Add(align);
Assert.IsTrue(AlignmentHelpers.CompareAlignment(result, expectedOutput,true));
ApplicationLog.WriteLine(string.Format(null, "PairwiseOverlapAligner P2 : Final Score '{0}'.", expectedScore));
ApplicationLog.WriteLine(string.Format(null, "PairwiseOverlapAligner P2 : Aligned First Sequence is '{0}'.", expectedSequence1));
ApplicationLog.WriteLine(string.Format(null, "PairwiseOverlapAligner P2 : Aligned Second Sequence is '{0}'.", expectedSequence2));
}
/// <summary>
/// Validates PairwiseOverlapAlignment algorithm for the parameters passed.
/// </summary>
/// <param name="nodeName">Node Name in the xml.</param>
/// <param name="alignParam">parameter based on which certain validations are done.</param>
private void ValidatePairwiseOverlapAlignment(string nodeName, AlignParameters alignParam)
{
this.ValidatePairwiseOverlapAlignment(nodeName, alignParam, SimilarityMatrixParameters.Default);
}
/// <summary>
/// Validates SmithWatermanAlignment algorithm for the parameters passed.
/// </summary>
/// <param name="nodeName">Node Name in the xml.</param>
/// <param name="alignParam">parameter based on which certain validations are done.</param>
/// <param name="similarityMatrixParam">Similarity Matrix Parameter.</param>
private void ValidateSmithWatermanAlignment(string nodeName, AlignParameters alignParam,
SimilarityMatrixParameters similarityMatrixParam)
{
this.ValidateSmithWatermanAlignment(nodeName, alignParam, similarityMatrixParam, AlignmentType.SimpleAlign);
}
/// <summary>
/// Validates SmithWatermanAlignment algorithm for the parameters passed.
/// </summary>
/// <param name="nodeName">Node Name in the xml.</param>
/// <param name="alignParam">parameter based on which certain validations are done.</param>
private void ValidateSmithWatermanAlignment(string nodeName, AlignParameters alignParam)
{
this.ValidateSmithWatermanAlignment(nodeName, alignParam, SimilarityMatrixParameters.Default);
}
private void ValidateNeedlemanWunschAlignment(string nodeName, AlignParameters alignParam,
SimilarityMatrixParameters similarityMatrixParam,
AlignmentType alignType)
{
ISequence aInput, bInput;
IAlphabet alphabet =
Utility.GetAlphabet(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.AlphabetNameNode));
// Parse the files and get the sequence.
if (alignParam.ToString().Contains("Code"))
{
string sequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceNode1);
string sequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceNode2);
aInput = new Sequence(alphabet, sequence1);
bInput = new Sequence(alphabet, sequence2);
}
else
{
// Read the xml file for getting both the files for aligning.
string filePath1 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode1);
string filePath2 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode2);
var parseObjectForFile1 = new FastAParser { Alphabet = alphabet };
ISequence originalSequence1 = parseObjectForFile1.Parse(filePath1).FirstOrDefault();
Assert.IsNotNull(originalSequence1);
aInput = new Sequence(alphabet, originalSequence1.ConvertToString());
var parseObjectForFile2 = new FastAParser { Alphabet = alphabet };
ISequence originalSequence2 = parseObjectForFile2.Parse(filePath2).FirstOrDefault();
Assert.IsNotNull(originalSequence2);
bInput = new Sequence(alphabet, originalSequence2.ConvertToString());
}
string blosumFilePath = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.BlosumFilePathNode);
SimilarityMatrix sm;
switch (similarityMatrixParam)
{
case SimilarityMatrixParameters.TextReader:
using (TextReader reader = new StreamReader(blosumFilePath))
sm = new SimilarityMatrix(reader);
break;
case SimilarityMatrixParameters.DiagonalMatrix:
string matchValue = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.MatchScoreNode);
string misMatchValue = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.MisMatchScoreNode);
sm = new DiagonalSimilarityMatrix(int.Parse(matchValue, null),
int.Parse(misMatchValue, null));
break;
default:
sm = new SimilarityMatrix(new StreamReader(blosumFilePath));
break;
}
int gapOpenCost = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.GapOpenCostNode), null);
int gapExtensionCost = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.GapExtensionCostNode),
null);
var needlemanWunschObj = new NeedlemanWunschAligner();
if (AlignParameters.AllParam != alignParam)
{
needlemanWunschObj.SimilarityMatrix = sm;
needlemanWunschObj.GapOpenCost = gapOpenCost;
}
IList<IPairwiseSequenceAlignment> result = null;
switch (alignParam)
{
case AlignParameters.AlignList:
case AlignParameters.AlignListCode:
var sequences = new List<ISequence> {aInput, bInput};
switch (alignType)
{
case AlignmentType.Align:
needlemanWunschObj.GapExtensionCost = gapExtensionCost;
result = needlemanWunschObj.Align(sequences);
break;
default:
result = needlemanWunschObj.AlignSimple(sequences);
break;
}
break;
case AlignParameters.AllParam:
case AlignParameters.AllParamCode:
switch (alignType)
{
case AlignmentType.Align:
needlemanWunschObj.GapExtensionCost = gapExtensionCost;
result = needlemanWunschObj.Align(sm,
gapOpenCost, gapExtensionCost, aInput, bInput);
break;
default:
result = needlemanWunschObj.AlignSimple(sm, gapOpenCost, aInput, bInput);
break;
}
break;
case AlignParameters.AlignTwo:
case AlignParameters.AlignTwoCode:
switch (alignType)
{
case AlignmentType.Align:
needlemanWunschObj.GapExtensionCost = gapExtensionCost;
result = needlemanWunschObj.Align(aInput, bInput);
break;
default:
result = needlemanWunschObj.AlignSimple(aInput, bInput);
break;
}
break;
default:
break;
}
// Read the xml file for getting both the files for aligning.
string expectedSequence1, expectedSequence2, expectedScore;
switch (alignType)
{
case AlignmentType.Align:
expectedScore = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedGapExtensionScoreNode);
expectedSequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedGapExtensionSequence1Node);
expectedSequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedGapExtensionSequence2Node);
break;
default:
expectedScore = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedScoreNode);
expectedSequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequenceNode1);
expectedSequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequenceNode2);
break;
}
IList<IPairwiseSequenceAlignment> expectedOutput = new List<IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment align = new PairwiseSequenceAlignment(aInput, bInput);
var alignedSeq = new PairwiseAlignedSequence
{
FirstSequence = new Sequence(alphabet, expectedSequence1),
SecondSequence = new Sequence(alphabet, expectedSequence2),
Score = Convert.ToInt32(expectedScore, null)
};
align.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(align);
ApplicationLog.WriteLine(string.Format("NeedlemanWunschAligner P1 : Final Score '{0}'.", expectedScore));
ApplicationLog.WriteLine(string.Format("NeedlemanWunschAligner P1 : Aligned First Sequence is '{0}'.", expectedSequence1));
ApplicationLog.WriteLine(string.Format("NeedlemanWunschAligner P1 : Aligned Second Sequence is '{0}'.", expectedSequence2));
Assert.IsTrue(CompareAlignment(result, expectedOutput));
}
/// <summary>
/// Validates NeedlemanWunschAlignment algorithm for the parameters passed.
/// </summary>
/// <param name="nodeName">Node Name in the xml.</param>
/// <param name="alignParam">parameter based on which certain validations are done.</param>
/// <param name="similarityMatrixParam">Similarity Matrix Parameter.</param>
private void ValidateNeedlemanWunschAlignment(string nodeName, AlignParameters alignParam,
SimilarityMatrixParameters similarityMatrixParam)
{
this.ValidateNeedlemanWunschAlignment(nodeName, alignParam, similarityMatrixParam, AlignmentType.SimpleAlign);
}
/// <summary>
/// Validates NeedlemanWunschAlignment algorithm for the parameters passed.
/// </summary>
/// <param name="nodeName">Node Name in the xml.</param>
/// <param name="alignParam">parameter based on which certain validations are done.</param>
private void ValidateNeedlemanWunschAlignment(string nodeName, AlignParameters alignParam)
{
this.ValidateNeedlemanWunschAlignment(nodeName, alignParam, SimilarityMatrixParameters.Default);
}
