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; }