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 InValidateGenBankLocations()
{
// Build a location with invalid values
ILocationBuilder locBuilder = new LocationBuilder();
ILocation loc = null;
try
{
loc = locBuilder.GetLocation(null);
Assert.Fail();
}
catch (ArgumentNullException)
{
Assert.IsNull(loc);
ApplicationLog.WriteLine(
"GenBankFeatures P2 : Validated the expected exception");
}
try
{
loc = locBuilder.GetLocation("Invalid");
Assert.Fail();
}
catch (ArgumentException)
{
Assert.IsNull(loc);
ApplicationLog.WriteLine(
"GenBankFeatures P2 : Validated the expected exception");
}
}
public void InValidateGenBankLocationPositions()
{
// Get Values from XML node.
string location = utilityObj.xmlUtil.GetTextValue(
Constants.LocationWithEndDataUsingOperatorNode, Constants.Location);
string expectedEndData = utilityObj.xmlUtil.GetTextValue(
Constants.LocationWithEndDataUsingOperatorNode, Constants.EndData);
string expectedStartData = utilityObj.xmlUtil.GetTextValue(
Constants.LocationWithEndDataUsingOperatorNode, Constants.StartData);
string position = utilityObj.xmlUtil.GetTextValue(
Constants.LocationWithEndDataUsingOperatorNode, Constants.Position);
// Build a location.
ILocationBuilder locBuilder = new LocationBuilder();
Location loc = (Location)locBuilder.GetLocation(location);
loc.Resolver = null;
loc.EndData = expectedEndData;
loc.StartData = expectedStartData;
// Validate whether mentioned end data is present in the location
// or not.
try
{
loc.IsInEnd(Int32.Parse(position, (IFormatProvider)null));
Assert.Fail();
}
catch (InvalidOperationException)
{
// Log to VSTest GUI.
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"GenBankFeatures P2 : Expected exception is verified"));
}
try
{
loc.IsInStart(Int32.Parse(position, (IFormatProvider)null));
Assert.Fail();
}
catch (InvalidOperationException)
{
// Log to VSTest GUI.
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"GenBankFeatures P2 : Expected exception is verified"));
}
try
{
loc.IsInRange(Int32.Parse(position, (IFormatProvider)null));
Assert.Fail();
}
catch (InvalidOperationException)
{
// Log to VSTest GUI.
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"GenBankFeatures P2 : Expected exception is verified"));
}
}
public void InValidateSubSequenceWithInvalidAccessionID()
{
// Get Values from XML node.
string sequence = utilityObj.xmlUtil.GetTextValue(
Constants.LocationWithDotOperatorNode,
Constants.ExpectedSequence);
string location = utilityObj.xmlUtil.GetTextValue(
Constants.LocationWithDotOperatorNode,
Constants.Location);
string alphabet = utilityObj.xmlUtil.GetTextValue(
Constants.LocationWithDotOperatorNode,
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);
loc.Accession = "Invalid";
// Get sequence using location of the sequence with operator.
try
{
loc.GetSubSequence(seqObj);
Assert.Fail();
}
catch (ArgumentException)
{
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"GenBankFeatures P2 : Validate the exception successfully"));
}
Dictionary<string, ISequence> refSeq = null;
// Validate GetSubSequence method with null location.
try
{
loc.GetSubSequence(null, refSeq);
Assert.Fail();
}
catch (ArgumentNullException)
{
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"GenBankFeatures P2 : Validate the exception successfully"));
}
}
/// <summary>
/// Validate general Location builder.
/// </summary>
/// <param name="operatorPam">Different operator parameter name</param>
/// <param name="nodeName">Different location string node name</param>
/// <param name="isOperator">True if operator else false.</param>
private void ValidateLocationBuilder(string nodeName,
LocationOperatorParameter operatorPam, bool isOperator)
{
// Get Values from XML node.
string locationString = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LocationStringValue);
string locationStartPosition = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LoocationStartNode);
string locationEndPosition = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LoocationEndNode);
string locationSeperatorNode = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LocationSeperatorNode);
string expectedLocationString = string.Empty;
string sublocationStartPosition = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.SubLocationStart);
string sublocationEndPosition = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.SubLocationEnd);
string sublocationSeperatorNode = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.SubLocationSeperator);
string subLocationsCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.SubLocationCount);
// Build a new location
ILocationBuilder locationBuilderObj = new LocationBuilder();
ILocation location = locationBuilderObj.GetLocation(locationString);
expectedLocationString = locationBuilderObj.GetLocationString(location);
// Validate constructed location starts,end and location string.
Assert.AreEqual(locationStartPosition, location.LocationStart.ToString((IFormatProvider) null));
Assert.AreEqual(locationString, expectedLocationString);
Assert.AreEqual(locationEndPosition, location.LocationEnd.ToString((IFormatProvider) null));
switch (operatorPam)
{
case LocationOperatorParameter.Join:
Assert.AreEqual(LocationOperator.Join, location.Operator);
break;
case LocationOperatorParameter.Complement:
Assert.AreEqual(LocationOperator.Complement, location.Operator);
break;
case LocationOperatorParameter.Order:
Assert.AreEqual(LocationOperator.Order, location.Operator);
break;
default:
Assert.AreEqual(LocationOperator.None, location.Operator);
Assert.AreEqual(locationSeperatorNode,
location.Separator.ToString(null));
Assert.IsTrue(string.IsNullOrEmpty(location.Accession));
Assert.IsNotNull(location.SubLocations);
break;
}
if (isOperator)
{
Assert.IsTrue(string.IsNullOrEmpty(location.Separator));
Assert.AreEqual(sublocationEndPosition,
location.SubLocations[0].LocationEnd.ToString((IFormatProvider) null));
Assert.AreEqual(sublocationSeperatorNode,
location.SubLocations[0].Separator.ToString(null));
Assert.AreEqual(Convert.ToInt32(subLocationsCount, null),
location.SubLocations.Count);
Assert.AreEqual(sublocationStartPosition,
location.SubLocations[0].LocationStart.ToString((IFormatProvider) null));
Assert.AreEqual(LocationOperator.None,
location.SubLocations[0].Operator);
Assert.AreEqual(0,
location.SubLocations[0].SubLocations.Count);
}
}
/// <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"));
}
/// <summary>
/// Validate Location builder and location resolver.
/// </summary>
/// <param name="nodeName">xml node name.</param>
/// <param name="FeatureOperator">Name of the operator used in a location</param>
/// <param name="isOperator">
/// True if location resolver validation with
/// operator
/// </param>
private void ValidateGenBankLocationResolver(string nodeName,
FeatureOperator operatorName, bool isOperator)
{
// Get Values from XML node.
string sequence = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequence);
string location = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Location);
string alphabet = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string expectedSeq = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExpSequenceWithOperator);
// Create a sequence object.
ISequence seqObj = new Sequence(Utility.GetAlphabet(alphabet),
sequence);
ISequence expectedSeqWithLoc;
// Build a location.
ILocationBuilder locBuilder = new LocationBuilder();
ILocation loc = locBuilder.GetLocation(location);
if (isOperator)
{
switch (operatorName)
{
case FeatureOperator.Complement:
loc.Operator = LocationOperator.Complement;
break;
case FeatureOperator.Join:
loc.Operator = LocationOperator.Join;
break;
case FeatureOperator.Order:
loc.Operator = LocationOperator.Order;
break;
default:
break;
}
}
// Get sequence using location of the sequence with operator.
expectedSeqWithLoc = loc.GetSubSequence(seqObj);
var sequenceString = new string(expectedSeqWithLoc.Select(a => (char) a).ToArray());
Assert.AreEqual(expectedSeq, sequenceString);
// Log to VSTest GUI.
ApplicationLog.WriteLine(string.Format(null,
"GenBankFeatures P1 : Expected sequence is verfied '{0}'.",
sequenceString));
}
public void ValidateCompareGenBankLocationsObject()
{
// Get Values from XML node.
string locationFirstInput = utilityObj.xmlUtil.GetTextValue(
Constants.CompareLocationsNode, Constants.Location1Node);
string locationSecondInput = utilityObj.xmlUtil.GetTextValue(
Constants.CompareLocationsNode, Constants.Location2Node);
string locationThirdInput = utilityObj.xmlUtil.GetTextValue(
Constants.CompareLocationsNode, Constants.Location3Node);
// Create two location instance.
ILocationBuilder locBuilder = new LocationBuilder();
ILocation loc1 = locBuilder.GetLocation(locationFirstInput);
object loc2 = locBuilder.GetLocation(locationSecondInput);
object loc3 = locBuilder.GetLocation(locationThirdInput);
// Compare first and second location instances.
Assert.AreEqual(0, loc1.CompareTo(loc2));
// Compare first and third location which are not identical.
Assert.AreEqual(-1, loc1.CompareTo(loc3));
// Compare first and null location.
Assert.AreEqual(1, loc1.CompareTo(null));
ApplicationLog.WriteLine(
"GenBank Features P1: Successfully validated the GenBank Features");
}