/// <summary>
/// Validate general segmented sequences methods
/// Add,Clear,replace,copyTo,Remove,Contains,Range,
/// Insert,IndexOf,Replace,RemoveAt,InsertRange,ReplaceRange.
/// <param name="nodeName">xml node name.</param
/// <param name="methodName">Method Name</param>
/// </summary>
void ValidateGeneralMethodsOfSegmentedSequence(
string nodeName, SegmentedSequenceParameters methodName)
{
// Gets the alphabet from the Xml
string alphabet = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string expectedSegSeqCount = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.SegmetedSeqCount);
string inputSequence1 = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.Sequence1);
string expectedSegmentedSeqAfterAddingNucleotide = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSeqAfterAdd);
string expectedSegmentedSeqCountAfterAddingNucleotide = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequenceCountAfterSeqAdd);
string expectedIndexValue = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.ExpectedIndexValue);
string insertSeq = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.InsertSeq);
string expectedInsertSeq = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.ExpectedInsertSeq);
string expectedRangeSeq = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.RangeSeq);
string expectedSeqAfterRemoveSeqItem = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.SequenceAfterRemove);
string expectedSeqAfterRemoveSeq = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.SeqAfterRemoveSeqRange);
string expectedSeqAfterReplace = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.SequenceAfterReplace);
string expectedSeqAfterReplaceSeqRange = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.SequenceAfterReplaceRange);
int index = 0;
int j = 1;
string expectedSeqAfterInsert = inputSequence1[0] + inputSequence1;
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.IsTrue(string.IsNullOrEmpty(segmentedSeq.ToString()));
break;
case SegmentedSequenceParameters.CopyTo:
// Copy sequence items to array.
ISequenceItem[] iseqItems = new ISequenceItem[895990];
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, (IFormatProvider)null) - j);
j++;
index++;
Console.WriteLine(string.Format((IFormatProvider)null,
"Segmented Sequence P1: Segmented Sequence{0} is as expected.",
segmentedSeq.ToString()));
}
break;
case SegmentedSequenceParameters.Contains:
//Validate wheather sequence item present in the segmented sequence
foreach (ISequenceItem item in seq)
{
bool seqItemPresent = segmentedSeq.Contains(seq[index]);
Assert.IsTrue(seqItemPresent);
index++;
}
break;
case SegmentedSequenceParameters.GetEnumerator:
//Get enumerator of the segmented sequence.
IEnumerator <ISequenceItem> segSeqEnumerator = segmentedSeq.GetEnumerator();
Assert.IsNotNull(segSeqEnumerator);
break;
case SegmentedSequenceParameters.IndexOf:
// Validate index of seg sequence items.
int indexValue = segmentedSeq.IndexOf(seq[6]);
Assert.AreEqual(indexValue, Convert.ToInt32(expectedIndexValue, (IFormatProvider)null));
break;
case SegmentedSequenceParameters.InsertChar:
// Validate insertion of sequence items in segmeted sequence.
segmentedSeq.Insert(0, inputSequence1[0]);
Assert.AreEqual(segmentedSeq.ToString(), expectedSeqAfterInsert);
Assert.AreEqual(segmentedSeq.Count, Convert.ToInt32(expectedSegSeqCount, (IFormatProvider)null) + 1);
break;
case SegmentedSequenceParameters.InsertRange:
// Validate insertion of sequence items in segmeted sequence.
segmentedSeq.InsertRange(10, insertSeq);
Assert.AreEqual(segmentedSeq.ToString(), expectedInsertSeq);
Assert.AreEqual(segmentedSeq.Count,
Convert.ToInt32(expectedSegSeqCount, (IFormatProvider)null) + insertSeq.Length);
break;
case SegmentedSequenceParameters.Range:
// Validate range of segmented sequence.
ISequence rangeSeq = segmentedSeq.Range(20, 20);
Assert.AreEqual(rangeSeq.ToString(), expectedRangeSeq);
break;
case SegmentedSequenceParameters.RemoveAt:
// Validate range of segmented sequence.
segmentedSeq.RemoveAt(70);
Assert.AreEqual(segmentedSeq.ToString(), expectedSeqAfterRemoveSeqItem);
break;
case SegmentedSequenceParameters.RemoveRange:
// Validate range of segmented sequence.
segmentedSeq.RemoveRange(0, 10);
Assert.AreEqual(segmentedSeq.ToString(), expectedSeqAfterRemoveSeq);
break;
case SegmentedSequenceParameters.ToString:
// Validate Tostring.
Assert.AreEqual(segmentedSeq.ToString(), inputSequence1);
break;
case SegmentedSequenceParameters.ReplaceChar:
// Validate replacement of sequence items in segmeted sequence.
segmentedSeq.Replace(15, inputSequence1[0]);
Assert.AreEqual(segmentedSeq.ToString(), expectedSeqAfterReplace);
break;
case SegmentedSequenceParameters.ReplaceRange:
// Validate replacement of sequence items in segmeted sequence.
segmentedSeq.ReplaceRange(0, insertSeq);
Assert.AreEqual(segmentedSeq.ToString(), expectedSeqAfterReplaceSeqRange);
break;
default:
break;
}
Console.WriteLine(string.Format((IFormatProvider)null,
"Segmented Sequence P1: Segmented Sequence{0} is as expected.",
segmentedSeq.ToString()));
Console.WriteLine(string.Format((IFormatProvider)null,
"Segmented Sequence P1: Segmented Sequence count{0} is as expected.",
segmentedSeq.Count.ToString((IFormatProvider)null)));
}
/// <summary>
/// General method to validate creation of Segmented seqeunce.
/// <param name="nodeName">xml node name.</param>
/// <param name="methodName">Method Name</param>
/// </summary>
void ValidateSegmentedSequenceCreation(
string nodeName, SegmentedSequenceParameters methodName,
bool IsCloneMethod)
{
// Gets the alphabet from the Xml
string alphabet = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string expectedSegmentedSeq = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequence);
string inputSequence1 = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.Sequence1);
string inputSequence2 = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.Sequence2);
string inputSequence3 = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.Sequence3);
string inputSequence4 = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.Sequence4);
string expectedSegSeqCount = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.SegmetedSeqCount);
string expectedSeguencesCount = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.SequencesCount);
ISequence seq = null;
List <ISequence> seqList = new List <ISequence>();
SegmentedSequence segmentedSeq = null;
ISequence segSeq = null;
// Logs information to the log file
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Segmented Sequence P1: Sequence {0} is expected.", alphabet));
switch (methodName)
{
case SegmentedSequenceParameters.SegmentedSeqList:
// create a Isequence.
ISequence seq1 = new Sequence(Utility.GetAlphabet(alphabet), inputSequence1);
ISequence seq2 = new Sequence(Utility.GetAlphabet(alphabet), inputSequence2);
ISequence seq3 = new Sequence(Utility.GetAlphabet(alphabet), inputSequence3);
ISequence seq4 = new Sequence(Utility.GetAlphabet(alphabet), inputSequence4);
// Add all sequences to sequence list.
seqList.Add(seq1);
seqList.Add(seq2);
seqList.Add(seq3);
seqList.Add(seq4);
// create a Segmented seqeunce 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]);
Console.WriteLine(string.Format((IFormatProvider)null,
"Segmented Sequence P1: Segmented Sequence{0} is as expected.",
segmentedSeq.ToString()));
break;
case SegmentedSequenceParameters.SegmentedSeq:
// create a Isequence.
seq = new Sequence(Utility.GetAlphabet(alphabet), inputSequence1);
// create a Segmented seqeunce
segmentedSeq = new SegmentedSequence(seq);
// validate expected segmented sequence.
Assert.AreEqual(seq.ToString(), segmentedSeq.ToString());
Console.WriteLine(string.Format((IFormatProvider)null,
"Segmented Sequence P1: Segmented Sequence{0} is as expected.",
segmentedSeq.ToString()));
break;
case SegmentedSequenceParameters.Clone:
// create a Isequence.
seq = new Sequence(Utility.GetAlphabet(alphabet), inputSequence1);
segSeq = new SegmentedSequence(seq);
ICloneable cloneableSegSeq = new SegmentedSequence(seq);
// Create a copy of segmented sequence and validate.
ISequence cloneSeq = segSeq.Clone();
object iCloneSegSeq = cloneableSegSeq.Clone();
Assert.AreEqual(cloneSeq.ToString(), segSeq.ToString());
Assert.AreEqual(iCloneSegSeq.ToString(), segSeq.ToString());
Console.WriteLine(string.Format((IFormatProvider)null,
"Segmented Sequence P1: Segmented Sequence{0} is as expected.",
cloneSeq.ToString()));
break;
default:
break;
}
if (!IsCloneMethod)
{
// Validate the 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((IFormatProvider)null,
"Segmented Sequence P1: Segmented Sequence count{0} is as expected.",
segmentedSeq.Sequences.Count.ToString((IFormatProvider)null)));
Console.WriteLine(string.Format((IFormatProvider)null,
"Segmented Sequence P1: Segmented Sequences count{0} is as expected.",
segmentedSeq.Count.ToString((IFormatProvider)null)));
// Logs to the NUnit GUI (Console.Out) window
ApplicationLog.WriteLine(
"Segmented Sequence P1: Segmented Sequence validation is completed successfully.");
}
}
