/// <summary>
/// Validate general segmented sequence methods such as
/// Add,Clear,replace,copyTo,Remove.
/// <param name="nodeName">xml node name.</param
/// <param name="methodName">Method Name</param>
/// </summary>
static void ValidateGeneralMethodsOfSegmentedSequence(
string nodeName, segmentedSequenceParameters methodName)
{
// Gets the alphabet from the Xml
string alphabet = Utility._xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string expectedSegSeqCount = Utility._xmlUtil.GetTextValue(
nodeName, Constants.SegmetedSeqCount);
string inputSequence1 = Utility._xmlUtil.GetTextValue(
nodeName, Constants.Sequence1);
string expectedSegmentedSeqAfterAddingNucleotide = Utility._xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSeqAfterAdd);
string expectedSegmentedSeqCountAfterAddingNucleotide = Utility._xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequenceCountAfterSeqAdd);
string inputSequence3 = Utility._xmlUtil.GetTextValue(
nodeName, Constants.Sequence3);
int index = 0;
int j = 1;
Sequence seq = null;
SegmentedSequence segmentedSeq = null;
// create a Isequence.
seq = new Sequence(Utility.GetAlphabet(alphabet), inputSequence1);
seq.IsReadOnly = false;
// create a Segmented seqeunce
segmentedSeq = new SegmentedSequence(seq);
Assert.AreEqual(seq.ToString(), segmentedSeq.ToString());
switch (methodName)
{
case segmentedSequenceParameters.Add:
// Add all sequence items to the end of the sequence.
foreach (ISequenceItem item in Utility.GetAlphabet(alphabet))
{
segmentedSeq.Add(item);
}
// validate segmented sequence after adding sequence item.
Assert.AreEqual(segmentedSeq.ToString(),
expectedSegmentedSeqAfterAddingNucleotide);
Assert.AreEqual(segmentedSeq.Count.ToString((IFormatProvider)null),
expectedSegmentedSeqCountAfterAddingNucleotide);
break;
case segmentedSequenceParameters.Clear:
// Clear all sequence items in segmented sequence.
segmentedSeq.Clear();
// validate segmented sequence after adding sequence item.
Assert.IsEmpty(segmentedSeq.ToString());
break;
case segmentedSequenceParameters.CopyTo:
// Copy sequence items to array.
ISequenceItem[] iseqItems = new ISequenceItem[140];
segmentedSeq.CopyTo(iseqItems, index);
Assert.IsNotNull(iseqItems);
// Validate array.
foreach (ISequenceItem item in Utility.GetAlphabet(alphabet))
{
Assert.AreEqual(iseqItems[index], segmentedSeq[index]);
Assert.AreEqual(iseqItems[index], segmentedSeq[index]);
Assert.AreEqual(iseqItems[index].Symbol, segmentedSeq[index].Symbol);
index++;
}
break;
case segmentedSequenceParameters.Remove:
//Remove sequence items in segmented sequence.
foreach (ISequenceItem item in segmentedSeq)
{
segmentedSeq.Remove(segmentedSeq[index]);
Assert.AreEqual(segmentedSeq.Count, Convert.ToInt32(expectedSegSeqCount) - j);
j++;
index++;
Console.WriteLine(string.Format(null,
"Segmented Sequence BVT: Segmented Sequence{0} is as expected.",
segmentedSeq.ToString()));
}
break;
case segmentedSequenceParameters.ReplaceChar:
//Replace each sequence items with different.
foreach (ISequenceItem item in segmentedSeq)
{
segmentedSeq.Replace(index, inputSequence3[index]);
index++;
}
// Validate replaced character sequence.
Assert.AreEqual(segmentedSeq.ToString(), inputSequence3);
break;
default:
break;
}
Console.WriteLine(string.Format(null,
"Segmented Sequence BVT: Segmented Sequence{0} is as expected.",
segmentedSeq.ToString()));
Console.WriteLine(string.Format(null,
"Segmented Sequence BVT: Segmented Sequence count{0} is as expected.",
segmentedSeq.Count.ToString()));
}
/// <summary>
/// General method to validate creation of Segmented sequence.
/// <param name="nodeName">xml node name.</param>
/// <param name="methodName">Method Name</param>
/// </summary>
static void ValidateSegmentedsequenceCreation(
string nodeName, segmentedSequenceParameters methodName)
{
// Gets the alphabet from the Xml
string alphabet = Utility._xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string expectedSegmentedSeq = Utility._xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequence);
string inputSequence1 = Utility._xmlUtil.GetTextValue(
nodeName, Constants.Sequence1);
string inputSequence2 = Utility._xmlUtil.GetTextValue(
nodeName, Constants.Sequence2);
string inputSequence3 = Utility._xmlUtil.GetTextValue(
nodeName, Constants.Sequence3);
string inputSequence4 = Utility._xmlUtil.GetTextValue(
nodeName, Constants.Sequence4);
string inputSequence5 = Utility._xmlUtil.GetTextValue(
nodeName, Constants.Sequence5);
string inputSequence6 = Utility._xmlUtil.GetTextValue(
nodeName, Constants.Sequence6);
string inputSequence7 = Utility._xmlUtil.GetTextValue(
nodeName, Constants.Sequence7);
string expectedSegSeqCount = Utility._xmlUtil.GetTextValue(
nodeName, Constants.SegmetedSeqCount);
string expectedSeguencesCount = Utility._xmlUtil.GetTextValue(
nodeName, Constants.SequencesCount);
ISequence seq = null;
ISequence seq1 = null;
ISequence seq2 = null;
ISequence seq3 = null;
ISequence seq4 = null;
ISequence seq5 = null;
ISequence seq6 = null;
ISequence seq7 = null;
List <ISequence> seqList = new List <ISequence>();
SegmentedSequence segmentedSeq = null;
// Logs information to the log file
ApplicationLog.WriteLine(string.Format(null,
"Segmented Sequence BVT: Sequence {0} is expected.", alphabet));
// create a Isequence.
seq1 = new Sequence(Utility.GetAlphabet(alphabet), inputSequence1);
seq2 = new Sequence(Utility.GetAlphabet(alphabet), inputSequence2);
seq3 = new Sequence(Utility.GetAlphabet(alphabet), inputSequence3);
seq4 = new Sequence(Utility.GetAlphabet(alphabet), inputSequence4);
seq5 = new Sequence(Utility.GetAlphabet(alphabet), inputSequence5);
seq6 = new Sequence(Utility.GetAlphabet(alphabet), inputSequence6);
seq7 = new Sequence(Utility.GetAlphabet(alphabet), inputSequence7);
// Add all sequences to sequence list.
seqList.Add(seq1);
seqList.Add(seq2);
seqList.Add(seq3);
seqList.Add(seq4);
seqList.Add(seq5);
seqList.Add(seq6);
seqList.Add(seq7);
switch (methodName)
{
case segmentedSequenceParameters.SegmentedsequenceList:
// create a Segmented sequence with sequence list.
segmentedSeq = new SegmentedSequence(seqList);
// validate created segmented sequence list.
Assert.AreEqual(expectedSegmentedSeq, segmentedSeq.ToString());
Assert.AreSame(seq1, segmentedSeq.Sequences[0]);
Assert.AreSame(seq2, segmentedSeq.Sequences[1]);
Assert.AreSame(seq3, segmentedSeq.Sequences[2]);
Assert.AreSame(seq4, segmentedSeq.Sequences[3]);
Assert.AreSame(seq5, segmentedSeq.Sequences[4]);
Assert.AreSame(seq6, segmentedSeq.Sequences[5]);
Assert.AreSame(seq7, segmentedSeq.Sequences[6]);
Console.WriteLine(string.Format(null,
"Segmented Sequence BVT: Segmented Sequence{0} is as expected.",
segmentedSeq.ToString()));
break;
case segmentedSequenceParameters.SegmentedSequence:
// create a Isequence.
seq = new Sequence(Utility.GetAlphabet(alphabet), inputSequence1);
// create a Segmented sequence
segmentedSeq = new SegmentedSequence(seq);
// validate expected segmented sequence.
Assert.AreEqual(seq.ToString(), segmentedSeq.ToString());
Console.WriteLine(string.Format(null,
"Segmented Sequence BVT: Segmented Sequence{0} is as expected.",
segmentedSeq.ToString()));
break;
case segmentedSequenceParameters.Clone:
// create a Segmented sequence with sequence list.
segmentedSeq = new SegmentedSequence(seqList);
// create a segmented sequences clone.
SegmentedSequence segSequenceClone = segmentedSeq.Clone();
// validate Clone sequence.
Assert.AreEqual(segSequenceClone.ToString(), segmentedSeq.ToString());
Assert.AreEqual(segSequenceClone.Count, segmentedSeq.Count);
Assert.AreEqual(segSequenceClone.Sequences.Count, 7);
Console.WriteLine(string.Format(null,
"Segmented Sequence BVT: Segmented Sequence{0} is as expected.",
segmentedSeq.ToString()));
break;
default:
break;
}
// Validate a created segmented Sequence
Assert.AreEqual(segmentedSeq.Count.ToString((IFormatProvider)null),
expectedSegSeqCount);
Assert.AreEqual(segmentedSeq.Sequences.Count.ToString((IFormatProvider)null),
expectedSeguencesCount);
Assert.AreSame(Utility.GetAlphabet(alphabet), segmentedSeq.Alphabet);
// Logs to the NUnit GUI (Console.Out) window
Console.WriteLine(string.Format(null,
"Segmented Sequence BVT: Segmented Sequence count{0} is as expected.",
segmentedSeq.Sequences.Count.ToString((IFormatProvider)null)));
Console.WriteLine(string.Format(null,
"Segmented Sequence BVT: Segmented Sequences count{0} is as expected.",
segmentedSeq.Count.ToString((IFormatProvider)null)));
// Logs to the NUnit GUI (Console.Out) window
ApplicationLog.WriteLine(
"Segmented Sequence BVT: Segmented Sequence validation is completed successfully.");
}
