public void InValidateSubSequenceWithComplimentOperator()
{
// Get Values from XML node.
string sequence = utilityObj.xmlUtil.GetTextValue(
Constants.InvalidLocationWithComplementOperatorNode,
Constants.ExpectedSequence);
string location = utilityObj.xmlUtil.GetTextValue(
Constants.InvalidLocationWithComplementOperatorNode,
Constants.Location);
string alphabet = utilityObj.xmlUtil.GetTextValue(
Constants.InvalidLocationWithComplementOperatorNode,
Constants.AlphabetNameNode);
// Create a sequence object.
ISequence seqObj = new Sequence(Utility.GetAlphabet(alphabet),
sequence);
// Build a location.
ILocationBuilder locBuilder = new LocationBuilder();
ILocation loc = locBuilder.GetLocation(location);
LocationResolver locResolver = new LocationResolver();
// Get sequence using location of the sequence with operator.
try
{
loc.GetSubSequence(seqObj);
Assert.Fail();
}
catch (ArgumentException)
{
LogExceptionMessage();
}
// Validate sub sequence exception for an invalid sequence.
try
{
locResolver.GetSubSequence(loc, null);
Assert.Fail();
}
catch (ArgumentNullException)
{
LogExceptionMessage();
}
// Validate GetSubSequence method with null location.
try
{
locResolver.GetSubSequence(null, seqObj);
Assert.Fail();
}
catch (ArgumentNullException)
{
LogExceptionMessage();
}
// Validate sub sequence exception for an invalid sequence.
try
{
locResolver.GetSubSequence(loc, null, null);
Assert.Fail();
}
catch (ArgumentNullException)
{
LogExceptionMessage();
}
// Validate GetSubSequence method with null location.
try
{
locResolver.GetSubSequence(null, seqObj, null);
Assert.Fail();
}
catch (ArgumentNullException)
{
LogExceptionMessage();
}
// Validate GetSubSequence method with null location.
try
{
loc.GetSubSequence(null);
Assert.Fail();
}
catch (ArgumentNullException)
{
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"GenBankFeatures P2 : Validate the exception successfully"));
}
}
public void ValidateGenBankSubSequence()
{
// Get Values from XML node.
string filePath = utilityObj.xmlUtil.GetTextValue(
Constants.GenBankRepeatRegionQualifiersNode,
Constants.FilePathNode);
string expectedSubSequence = utilityObj.xmlUtil.GetTextValue(
Constants.GenBankRepeatRegionQualifiersNode,
Constants.ExpectedFeatureSubSequence);
// Parse a GenBank file.
ISequenceParser parserObj = new GenBankParser();
{
ISequence sequence = parserObj.ParseOne(filePath);
ILocationResolver locResolver = new LocationResolver();
// Get repeatregion subsequence.
var metadata =
(GenBankMetadata) sequence.Metadata[Constants.GenBank];
ISequence subSeq = locResolver.GetSubSequence(
metadata.Features.RepeatRegions[0].Location, sequence);
var sequenceString = new string(subSeq.Select(a => (char) a).ToArray());
// Validate repeat region subsequence.
Assert.AreEqual(sequenceString, expectedSubSequence);
// Log VSTest GUI.
ApplicationLog.WriteLine(
"GenBank Features P1: Successfully validated the GenBank subSequence");
}
}