public void TestAlignedSequenceToString()
{
IList <ISequence> seqList = new List <ISequence>();
seqList.Add(new Sequence(Alphabets.DNA, "CAAAAGGGATTGC---TGTTGGAGTGAATGCCATTACCTACCGGCTAGGAGGAGTAGTACAAAGGAGC"));
seqList.Add(new Sequence(Alphabets.DNA, "CAAAAGGGATTGC---"));
seqList.Add(new Sequence(Alphabets.DNA, "TAGTAGTTCTGCTATATACATTTG"));
seqList.Add(new Sequence(Alphabets.DNA, "GTTATCATGCGAACAATTCAACAGACACTGTAGA"));
NucmerPairwiseAligner num = new NucmerPairwiseAligner();
num.BreakLength = 8;
num.FixedSeparation = 0;
num.MinimumScore = 0;
num.MaximumSeparation = 0;
num.SeparationFactor = 0;
num.LengthOfMUM = 8;
IList <ISequence> sequenceList = seqList;
IList <ISequenceAlignment> alignmentObj = num.Align(sequenceList);
AlignedSequence alignedSeqs = (AlignedSequence)alignmentObj[0].AlignedSequences[0];
string actualString = alignedSeqs.ToString();
string expectedString = "CAAAAGGGATTGC---\r\nCAAAAGGGATTGC---\r\nCAAAAGGGATTGC---\r\n";
Assert.AreEqual(actualString, expectedString);
}
public void ValidateAlignedSequenceToString()
{
IList <ISequence> seqList = new List <ISequence>();
string actualAlignedSeqString = utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName,
Constants.AlignedSeqActualNode);
seqList.Add(new Sequence(Alphabets.DNA,
actualAlignedSeqString));
seqList.Add(new Sequence(Alphabets.DNA, "CAAAAGGGATTGC---"));
seqList.Add(new Sequence(Alphabets.DNA, "TAGTAGTTCTGCTATATACATTTG"));
seqList.Add(new Sequence(Alphabets.DNA, "GTTATCATGCGAACAATTCAACAGACACTGTAGA"));
NucmerPairwiseAligner num = new NucmerPairwiseAligner();
num.BreakLength = 8;
num.FixedSeparation = 0;
num.MinimumScore = 0;
num.MaximumSeparation = 0;
num.SeparationFactor = 0;
num.LengthOfMUM = 8;
IList <ISequence> sequenceList = seqList;
IList <ISequenceAlignment> alignmentObj = num.Align(sequenceList);
AlignedSequence alignedSeqs = (AlignedSequence)alignmentObj[0].AlignedSequences[0];
string actualString = alignedSeqs.ToString();
string expectedString = utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName,
Constants.AlignedSeqExpectedNode);
Assert.AreEqual(actualString.Replace("\r\n", ""), expectedString.Replace("\\r\\n", ""));
}