public void ValidatePairwiseAlignmentAttributes()
{
var pwAlignAttrib = new PairwiseAlignmentAttributes();
Dictionary <string, AlignmentInfo> attributes = pwAlignAttrib.Attributes;
AlignmentInfo similarityMatrixObj = attributes["SIMILARITYMATRIX"];
AlignmentInfo gapOpenCostObj = attributes["GAPOPENCOST"];
AlignmentInfo gapExtensionCostObj = attributes["GAPEXTENSIONCOST"];
Assert.AreEqual("Similarity Matrix", similarityMatrixObj.Name);
var validator = new StringListValidator(
"Diagonal (Match x Mismatch)",
SimilarityMatrix.StandardSimilarityMatrix.AmbiguousDna.ToString(),
SimilarityMatrix.StandardSimilarityMatrix.AmbiguousRna.ToString(),
SimilarityMatrix.StandardSimilarityMatrix.Blosum45.ToString(),
SimilarityMatrix.StandardSimilarityMatrix.Blosum50.ToString(),
SimilarityMatrix.StandardSimilarityMatrix.Blosum62.ToString(),
SimilarityMatrix.StandardSimilarityMatrix.Blosum80.ToString(),
SimilarityMatrix.StandardSimilarityMatrix.Blosum90.ToString(),
SimilarityMatrix.StandardSimilarityMatrix.DiagonalScoreMatrix.ToString(),
SimilarityMatrix.StandardSimilarityMatrix.Pam250.ToString(),
SimilarityMatrix.StandardSimilarityMatrix.Pam30.ToString());
Assert.IsTrue(validator.IsValid(SimilarityMatrix.StandardSimilarityMatrix.AmbiguousDna.ToString()));
validator.AddValidValues(SimilarityMatrix.StandardSimilarityMatrix.Pam70.ToString());
Assert.AreEqual("Diagonal (Match x Mismatch)", validator.ValidValues[0]);
Assert.AreEqual("Gap Cost", gapOpenCostObj.Name);
Assert.AreEqual("Gap Extension Cost", gapExtensionCostObj.Name);
ApplicationLog.WriteLine(
"PairwiseAlignmentAttributes BVT: Successfully validated all the attributes.");
}
/// <summary>
/// Gets the list of alignment argument based on the algorithm selected
/// </summary>
/// <returns>Alignment arguments</returns>
private IAlignmentAttributes GetAlignmentAttribute(string algo)
{
IAlignmentAttributes alignmentAttributes = null;
ISequenceAligner sequenceAligner = ChooseAlgorithm(algo);
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();
}
else if (sequenceAligner is PAMSAMMultipleSequenceAligner)
{
alignmentAttributes = new PamsamAlignmentAttributes();
}
return(alignmentAttributes);
}
/// <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 NUCmer3)
{
alignmentAttributes = new NUCmerAttributes();
}
else if (sequenceAligner is MUMmer3)
{
alignmentAttributes = new MUMmerAttributes();
}
else if ((sequenceAligner is SmithWatermanAligner) ||
(sequenceAligner is NeedlemanWunschAligner) ||
(sequenceAligner is PairwiseOverlapAligner))
{
alignmentAttributes = new PairwiseAlignmentAttributes();
}
return(alignmentAttributes);
}
