/// <summary>
/// Validate Sequence Alignment Class General methods exception.
/// </summary>
/// <param name="nodeName">Node Name in the xml.</param>
/// <param name="methodName">Name of the SequenceAlignment method to be validated</param>
/// </summary>
static void InValidateSequenceAlignmentGeneralMethods(string nodeName,
SeqAlignmentMethods methodName)
{
// Read the xml file for getting both the files for aligning.
string origSequence1 = Utility._xmlUtil.GetTextValue(nodeName,
Constants.SequenceNode1);
string origSequence2 = Utility._xmlUtil.GetTextValue(nodeName,
Constants.SequenceNode2);
IAlphabet alphabet = Utility.GetAlphabet(Utility._xmlUtil.GetTextValue(nodeName,
Constants.AlphabetNameNode));
string readOnlyException = Utility._xmlUtil.GetTextValue(nodeName,
Constants.ReadOnlyExceptionNode);
string expectedGetObjectDataException = Utility._xmlUtil.GetTextValue(nodeName,
Constants.GetObjectDataNullErrorMessageNode);
string actualError = null;
StreamingContext context = new StreamingContext(StreamingContextStates.All);
// Create two sequences
ISequence aInput = new Sequence(alphabet, origSequence1);
ISequence bInput = new Sequence(alphabet, origSequence2);
// Add the sequences to the Sequence alignment object using AddSequence() method.
IList <IPairwiseSequenceAlignment> sequenceAlignmentObj =
new List <IPairwiseSequenceAlignment>();
PairwiseAlignedSequence alignSeq = new PairwiseAlignedSequence();
alignSeq.FirstSequence = aInput;
alignSeq.SecondSequence = bInput;
PairwiseSequenceAlignment seqAlignObj = new PairwiseSequenceAlignment(aInput, bInput);;
seqAlignObj.Add(alignSeq);
sequenceAlignmentObj.Add(seqAlignObj);
// Set SequenceAlignment IsReadOnly prpoerty to true.
seqAlignObj.IsReadOnly = true;
IList <PairwiseAlignedSequence> newAlignedSequences =
sequenceAlignmentObj[0].PairwiseAlignedSequences;
switch (methodName)
{
case SeqAlignmentMethods.Add:
try
{
seqAlignObj.Add(newAlignedSequences[0]);
}
catch (NotSupportedException ex)
{
actualError = ex.Message;
}
// Validate Error message
Assert.AreEqual(readOnlyException, actualError);
break;
case SeqAlignmentMethods.Clear:
try
{
seqAlignObj.Clear();
}
catch (NotSupportedException ex)
{
actualError = ex.Message;
}
// Validate Error message
Assert.AreEqual(readOnlyException, actualError);
break;
case SeqAlignmentMethods.Remove:
try
{
seqAlignObj.Remove(newAlignedSequences[0]);
}
catch (NotSupportedException ex)
{
actualError = ex.Message;
}
// Validate Error message
Assert.AreEqual(readOnlyException, actualError);
break;
case SeqAlignmentMethods.AddSequence:
try
{
seqAlignObj.AddSequence(newAlignedSequences[0]);
}
catch (NotSupportedException ex)
{
actualError = ex.Message;
}
// Validate Error message
Assert.AreEqual(readOnlyException, actualError);
break;
case SeqAlignmentMethods.GetObjectData:
try
{
seqAlignObj.GetObjectData(null, context);
}
catch (ArgumentNullException ex)
{
actualError = ex.Message;
}
// Validate Error message
Assert.AreEqual(expectedGetObjectDataException,
actualError.Replace("\r", "").Replace("\n", ""));
break;
default:
break;
}
ApplicationLog.WriteLine("SequenceAlignment P2 : Successfully validated the IsRead Property");
Console.WriteLine("SequenceAlignment P2 : Successfully validated the IsRead Property");
}
/// <summary>
/// Validates Sequence Alignment Class General methods.
/// </summary>
/// <param name="nodeName">Node Name in the xml.</param>
/// <param name="methodName">Name of the SequenceAlignment method to be validated</param>
/// <param name="isSeqAlignDefCtr">Is sequence alignment Def Constructor</param>
private void ValidateSequenceAlignmentGeneralMethods(string nodeName, SeqAlignmentMethods methodName,
bool isSeqAlignDefCtr)
{
// Read the xml file for getting both the files for aligning.
string origSequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceNode1);
string origSequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceNode2);
IAlphabet alphabet =
Utility.GetAlphabet(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.AlphabetNameNode));
string seqCount = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SeqCountNode);
string alignedSeqCountAfterAddSeq = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants
.AlignedSeqCountAfterAddAlignedSeqNode);
string arrayLength = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ArraySizeNode);
var alignedSeqItems = new PairwiseAlignedSequence[int.Parse(arrayLength, null)];
const int Index = 0;
// Create two sequences
ISequence aInput = new Sequence(alphabet, origSequence1);
ISequence bInput = new Sequence(alphabet, origSequence2);
// Add the sequences to the Sequence alignment object using AddSequence() method.
IList<IPairwiseSequenceAlignment> sequenceAlignmentObj = new List<IPairwiseSequenceAlignment>();
var alignSeq = new PairwiseAlignedSequence {FirstSequence = aInput, SecondSequence = bInput};
IPairwiseSequenceAlignment seqAlignObj = isSeqAlignDefCtr
? new PairwiseSequenceAlignment()
: new PairwiseSequenceAlignment(aInput, bInput);
seqAlignObj.Add(alignSeq);
sequenceAlignmentObj.Add(seqAlignObj);
IList<PairwiseAlignedSequence> newAlignedSequences =
sequenceAlignmentObj[0].PairwiseAlignedSequences;
switch (methodName)
{
case SeqAlignmentMethods.Add:
seqAlignObj.Add(alignSeq);
Assert.AreEqual(seqCount,
seqAlignObj.PairwiseAlignedSequences.Count.ToString((IFormatProvider) null));
break;
case SeqAlignmentMethods.Clear:
seqAlignObj.Clear();
Assert.AreEqual(0, seqAlignObj.PairwiseAlignedSequences.Count);
break;
case SeqAlignmentMethods.Contains:
Assert.IsTrue(seqAlignObj.Contains(newAlignedSequences[0]));
break;
case SeqAlignmentMethods.CopyTo:
seqAlignObj.CopyTo(alignedSeqItems, Index);
// Validate Copied array.
Assert.AreEqual(alignedSeqItems[Index].FirstSequence, seqAlignObj.FirstSequence);
Assert.AreEqual(alignedSeqItems[Index].SecondSequence, seqAlignObj.SecondSequence);
break;
case SeqAlignmentMethods.Remove:
seqAlignObj.Remove(newAlignedSequences[0]);
// Validate whether removed item is deleted from SequenceAlignment.
Assert.AreEqual(0, newAlignedSequences.Count);
break;
case SeqAlignmentMethods.AddSequence:
seqAlignObj.AddSequence(newAlignedSequences[0]);
// Validate SeqAlignObj after adding aligned sequence.
Assert.AreEqual(alignedSeqCountAfterAddSeq, seqAlignObj.Count.ToString((IFormatProvider) null));
break;
case SeqAlignmentMethods.GetEnumerator:
IEnumerator<PairwiseAlignedSequence> alignedSeqList = seqAlignObj.GetEnumerator();
// Aligned Sequence list after iterating through ailgnedSeq collection.
Assert.IsNotNull(alignedSeqList);
break;
default:
break;
}
ApplicationLog.WriteLine("SequenceAlignment P1 : Successfully validated the IsRead Property");
ApplicationLog.WriteLine("SequenceAlignment P1 : Successfully validated the Count Property");
ApplicationLog.WriteLine("SequenceAlignment P1 : Successfully validated the Sequences Property");
}
