public void ValidateDeltaAlignmentToString()
{
ISequence refSeq = new Sequence(Alphabets.DNA, "ATCGGGGGGGGAAAAAAATTTTCCCCGGGGG");
ISequence qrySeq = new Sequence(Alphabets.DNA, "GGGGG");
var delta = new DeltaAlignment(refSeq, qrySeq)
{
FirstSequenceEnd = 21, SecondSequenceEnd = 20
};
string actualString = delta.ToString();
string expectedString = this.utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName, Constants.DeltaAlignmentExpectedNode);
Assert.AreEqual(expectedString, actualString);
// Gets the expected sequence from the Xml
List <ISequence> seqsList;
string filePath = this.utilityObj.xmlUtil.GetTextValue(Constants.SimpleFastaNodeName, Constants.FilePathNode);
using (var reader = File.OpenRead(filePath))
{
var parser = new FastAParser();
{
parser.Alphabet = Alphabets.Protein;
seqsList = parser.Parse(reader).ToList();
}
}
delta = new DeltaAlignment(seqsList[0], qrySeq)
{
FirstSequenceEnd = 21, SecondSequenceStart = 20, QueryDirection = Cluster.ReverseDirection
};
actualString = delta.ToString();
expectedString = this.utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName, Constants.DeltaAlignmentExpected2Node);
Assert.AreEqual(expectedString, actualString);
}
public void TestDeltaAlignmentToString()
{
ISequence refSeq = new Sequence(Alphabets.DNA, "ATCGGGGGGGGAAAAAAATTTTCCCCGGGGG");
ISequence qrySeq = new Sequence(Alphabets.DNA, "GGGGG");
DeltaAlignment delta = new DeltaAlignment(refSeq, qrySeq);
delta.FirstSequenceEnd = 21;
delta.SecondSequenceEnd = 20;
string actualString = delta.ToString();
string expectedString = "Ref ID= Query Id= Ref start=0 Ref End=21 Query start=0 Query End=20, Direction=FORWARD";
Assert.AreEqual(actualString, expectedString);
}
public void ValidateDeltaAlignmentToString()
{
ISequence refSeq = new Sequence(Alphabets.DNA, "ATCGGGGGGGGAAAAAAATTTTCCCCGGGGG");
ISequence qrySeq = new Sequence(Alphabets.DNA, "GGGGG");
DeltaAlignment delta = new DeltaAlignment(refSeq, qrySeq);
delta.FirstSequenceEnd = 21;
delta.SecondSequenceEnd = 20;
string actualString = delta.ToString();
string expectedString = utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName,
Constants.DeltaAlignmentExpectedNode);
Assert.AreEqual(actualString, expectedString);
// Gets the expected sequence from the Xml
List <ISequence> seqsList;
IEnumerable <ISequence> sequences = null;
string filePath = utilityObj.xmlUtil.GetTextValue(Constants.SimpleFastaNodeName,
Constants.FilePathNode);
using (StreamReader reader = new StreamReader(filePath))
{
using (FastAParser parser = new FastAParser())
{
parser.Alphabet = Alphabets.Protein;
sequences = parser.Parse(reader);
//Create a list of sequences.
seqsList = sequences.ToList();
}
}
DeltaAlignment delta1 = new DeltaAlignment(seqsList[0], qrySeq);
delta1.FirstSequenceEnd = 21;
delta1.SecondSequenceEnd = 20;
string actualString1 = delta1.ToString();
string expectedString1 = utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName,
Constants.DeltaAlignmentExpected2Node);
Assert.AreEqual(expectedString1, actualString1);
}
