public void ValidateNUCmerAttributes()
{
NUCmerAttributes nucAttrib = new NUCmerAttributes();
Dictionary<string, AlignmentInfo> attributes = nucAttrib.Attributes;
Assert.AreEqual(9, attributes.Count);
// Validating all the NUCmer attributes
AlignmentInfo similarityMatrixObj = attributes["SIMILARITYMATRIX"];
AlignmentInfo gapOpenCostObj = attributes["GAPOPENCOST"];
AlignmentInfo gapExtensionCostObj = attributes["GAPEXTENSIONCOST"];
AlignmentInfo lenOfMumObj = attributes["LENGTHOFMUM"];
AlignmentInfo fixedSepObj = attributes["FIXEDSEPARATION"];
AlignmentInfo maxSepObj = attributes["MAXIMUMSEPARATION"];
AlignmentInfo minScoreObj = attributes["MINIMUMSCORE"];
AlignmentInfo sepFactorObj = attributes["SEPARATIONFACTOR"];
AlignmentInfo breakLengthObj = attributes["BREAKLENGTH"];
Assert.AreEqual("Similarity Matrix", similarityMatrixObj.Name);
Assert.AreEqual("Gap Cost", gapOpenCostObj.Name);
Assert.AreEqual("Gap Extension Cost", gapExtensionCostObj.Name);
Assert.AreEqual("Length of MUM", lenOfMumObj.Name);
Assert.AreEqual("Fixed Separation", fixedSepObj.Name);
Assert.AreEqual("Maximum Separation", maxSepObj.Name);
Assert.AreEqual("Minimum Score", minScoreObj.Name);
Assert.AreEqual("Separation Factor", sepFactorObj.Name);
Assert.AreEqual("Break Length", breakLengthObj.Name);
}
/// <summary>
/// Gets the list of alignment argument based on the algorithm selected
/// </summary>
/// <param name="algoName">Name of the algorithm used</param>
/// <returns>Alignment arguments</returns>
private IAlignmentAttributes GetAlignmentAttribute(string algoName)
{
IAlignmentAttributes alignmentAttributes = null;
ISequenceAligner sequenceAligner = ChooseAlgorithm(algoName);
this.Aligner = sequenceAligner;
if (sequenceAligner is NucmerPairwiseAligner)
{
alignmentAttributes = new NUCmerAttributes();
}
else if (sequenceAligner is MUMmerAligner)
{
alignmentAttributes = new MUMmerAttributes();
}
else if ((sequenceAligner is SmithWatermanAligner)
|| (sequenceAligner is NeedlemanWunschAligner)
|| (sequenceAligner is PairwiseOverlapAligner))
{
alignmentAttributes = new PairwiseAlignmentAttributes();
}
return alignmentAttributes;
}