/// <summary>
/// Gets the expected error message for invalid sequence type.
/// </summary>
/// <param name="nodeName">xml node</param>
/// <param name="sequenceType">invalid sequence type.</param>
/// <returns>Returns expected error message</returns>
private string GetExpectedErrorMeesageWithInvalidSequenceType(string nodeName, InvalidSequenceType sequenceType)
{
string expectedErrorMessage = string.Empty;
switch (sequenceType)
{
case InvalidSequenceType.SequenceWithInvalidChars:
expectedErrorMessage = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.EmptySequenceErrorMessage);
break;
case InvalidSequenceType.InvalidSequence:
expectedErrorMessage = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.InvalidSequenceErrorMessage);
break;
case InvalidSequenceType.SequenceWithUnicodeChars:
expectedErrorMessage = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.UnicodeSequenceErrorMessage);
break;
case InvalidSequenceType.SequenceWithSpaces:
expectedErrorMessage = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.SequenceWithSpaceErrorMessage);
break;
case InvalidSequenceType.AlphabetMap:
expectedErrorMessage = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.InvalidAlphabetErrorMessage);
break;
default:
expectedErrorMessage = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedErrorMessage);
break;
}
return expectedErrorMessage;
}
/// <summary>
/// Gets the input file name for a given invalid sequence type.
/// </summary>
/// <param name="nodeName">xml node.</param>
/// <param name="invalidSequenceType"></param>
/// <returns>Returns input file name.</returns>
private string GetInputFileNameWithInvalidType(string nodeName,
InvalidSequenceType invalidSequenceType)
{
string invalidFilePath = string.Empty;
switch (invalidSequenceType)
{
case InvalidSequenceType.SequenceWithSpecialChars:
invalidFilePath = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.InvalidFilePathNode1);
break;
case InvalidSequenceType.EmptySequence:
invalidFilePath = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.EmptyFilePath1);
break;
case InvalidSequenceType.SequenceWithSpaces:
invalidFilePath = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SpacesFilePath1);
break;
case InvalidSequenceType.SequenceWithGap:
invalidFilePath = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.GapFilePath1);
break;
case InvalidSequenceType.SequenceWithUnicodeChars:
invalidFilePath = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.UnicodeFilePath1);
break;
default:
break;
}
return invalidFilePath;
}
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));
}
