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"));
}
}
/// <summary>
/// InValidate GenBank location with invalid Start location data.
/// <param name="endData">Start data used for different test cases.</param>
/// </summary>
private static void InValidateLocationStartData(string startData)
{
// Build a location.
LocationResolver locResolver = new LocationResolver();
string location = "123.125";
ILocationBuilder locBuilder = new LocationBuilder();
ILocation loc = locBuilder.GetLocation(location);
// Set Invalid end data Validate GetStart method exception.
loc.StartData = startData;
try
{
locResolver.IsInStart(loc, 124);
Assert.Fail();
}
catch (IndexOutOfRangeException)
{
LogExceptionMessage();
}
catch (FormatException)
{
LogExceptionMessage();
}
}
public void InValidateGenBankLocationEndData()
{
// Get Values from XML node.
string position = utilityObj.xmlUtil.GetTextValue(
Constants.LocationWithEndDataNode, Constants.Position);
// Build a location.
LocationResolver locResolver = new LocationResolver();
// Validate whether mentioned end data is present in the location
// or not.
try
{
locResolver.IsInEnd(null, Int32.Parse(position, (IFormatProvider)null));
Assert.Fail();
}
catch (ArgumentNullException)
{
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"GenBankFeatures P2 : Validate the exception successfully"));
}
// Validate IsInStart method exception.
try
{
locResolver.IsInStart(null, Int32.Parse(position, (IFormatProvider)null));
Assert.Fail();
}
catch (ArgumentNullException)
{
LogExceptionMessage();
}
// Validate IsInRange method exception.
try
{
locResolver.IsInRange(null, Int32.Parse(position, (IFormatProvider)null));
Assert.Fail();
}
catch (ArgumentNullException)
{
LogExceptionMessage();
}
}
public void InValidateGenBankLocationGetStart()
{
// Build a location.
LocationResolver locResolver = new LocationResolver();
// Validate GetStart method exception.
try
{
locResolver.GetStart(null);
Assert.Fail();
}
catch (ArgumentNullException)
{
LogExceptionMessage();
}
// Validate GetEnd method exception.
try
{
locResolver.GetEnd(null);
Assert.Fail();
}
catch (ArgumentNullException)
{
LogExceptionMessage();
}
}
/// <summary>
/// Default constructor.
/// </summary>
public Location()
{
SubLocations = new List <ILocation>();
Resolver = new LocationResolver();
}
/// <summary>
/// Default constructor.
/// </summary>
public Location()
{
SubLocations = new List<ILocation>();
Resolver = new LocationResolver();
}
/// <summary>
/// Validate location resolver end data.
/// </summary>
/// <param name="nodeName">xml node name.</param>
private void ValidateLocationEndData(string nodeName)
{
// Get Values from XML node.
string location = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Location);
string expectedEndData = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EndData);
string position = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Position);
bool result = false;
// Build a location.
var locResolver = new LocationResolver();
ILocationBuilder locBuilder = new LocationBuilder();
ILocation loc = locBuilder.GetLocation(location);
loc.EndData = expectedEndData;
// Validate whether mentioned end data is present in the location
// or not.
result = locResolver.IsInEnd(loc, Int32.Parse(position, null));
Assert.IsTrue(result);
// Log to VSTest GUI.
ApplicationLog.WriteLine(string.Format(null,
"GenBankFeatures P1 : Expected sequence is verified"));
}
public void ValidateGenBankLocationStartAndEndRange()
{
// Get Values from XML node.
string filePath = utilityObj.xmlUtil.GetTextValue(
Constants.GenBankRepeatRegionQualifiersNode,
Constants.FilePathNode);
bool startLocResult = false;
bool endLocResult = false;
bool rangeLocResult = false;
// Parse a GenBank file.
ISequenceParser parserObj = new GenBankParser();
{
ISequence sequence = parserObj.ParseOne(filePath);
ILocationResolver locResolver = new LocationResolver();
// Validate Start,End and Range of Gene feature location.
var metadata =
(GenBankMetadata) sequence.Metadata[Constants.GenBank];
startLocResult =
locResolver.IsInStart(metadata.Features.Genes[0].Location, 289);
endLocResult =
locResolver.IsInEnd(metadata.Features.Genes[0].Location, 1647);
rangeLocResult =
locResolver.IsInRange(metadata.Features.Genes[0].Location, 300);
Assert.IsTrue(startLocResult);
Assert.IsTrue(endLocResult);
Assert.IsTrue(rangeLocResult);
// Log VSTest GUI.
ApplicationLog.WriteLine(
"GenBank Features P1: Successfully validated the location resolver Gene feature start End and IsInRange methods");
}
}
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");
}
}
