/// <summary>
/// Private constructor for clone method.
/// </summary>
/// <param name="other">Other MiscDifference instance.</param>
private MiscDifference(MiscDifference other)
: base(other) { }
/// <summary>
/// Private constructor for clone method.
/// </summary>
/// <param name="other">Other MiscDifference instance.</param>
private MiscDifference(MiscDifference other)
: base(other)
{
}
/// <summary>
/// Validate GenBank Misc difference feature qualifiers.
/// </summary>
/// <param name="nodeName">xml node name.</param>
private void ValidateGenBankMiscDiffFeatureQualifiers(string nodeName)
{
// Get Values from XML node.
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string expectedMiscDiffCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.MiscDiffCount);
string expectedGeneSymbol = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSymbol);
// Parse a GenBank file.
ISequenceParser parserObj = new GenBankParser();
{
IEnumerable<ISequence> seqList = parserObj.Parse(filePath);
// Validate Protein feature all qualifiers.
var metadata =
(GenBankMetadata) seqList.ElementAt(1).Metadata[Constants.GenBank];
List<MiscDifference> miscDifferenceFeatureList =
metadata.Features.MiscDifferences;
Assert.AreEqual(miscDifferenceFeatureList.Count.ToString((IFormatProvider) null),
expectedMiscDiffCount);
Assert.AreEqual(miscDifferenceFeatureList[0].GeneSymbol,
expectedGeneSymbol);
Assert.IsTrue(string.IsNullOrEmpty(miscDifferenceFeatureList[0].Allele));
Assert.IsFalse(string.IsNullOrEmpty(miscDifferenceFeatureList[0].Citation.ToString()));
Assert.IsFalse(string.IsNullOrEmpty(miscDifferenceFeatureList[0].Experiment.ToString()));
Assert.IsFalse(string.IsNullOrEmpty(miscDifferenceFeatureList[0].GeneSynonym.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(miscDifferenceFeatureList[0].GenomicMapPosition));
Assert.IsFalse(string.IsNullOrEmpty(miscDifferenceFeatureList[0].Inference.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(miscDifferenceFeatureList[0].Label));
Assert.IsFalse(string.IsNullOrEmpty(miscDifferenceFeatureList[0].OldLocusTag.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(miscDifferenceFeatureList[0].StandardName));
Assert.IsTrue(string.IsNullOrEmpty(miscDifferenceFeatureList[0].Replace));
Assert.IsFalse(string.IsNullOrEmpty(miscDifferenceFeatureList[0].Phenotype.ToString()));
Assert.IsFalse(string.IsNullOrEmpty(miscDifferenceFeatureList[0].OldLocusTag.ToString()));
Assert.IsFalse(string.IsNullOrEmpty(miscDifferenceFeatureList[0].LocusTag.ToString()));
Assert.IsFalse(string.IsNullOrEmpty(miscDifferenceFeatureList[0].Compare.ToString()));
Assert.IsFalse(string.IsNullOrEmpty(miscDifferenceFeatureList[0].DatabaseCrossReference.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(miscDifferenceFeatureList[0].ClonedFrom));
// Create a new MiscDiff feature using constructor.
var miscDiffWithLoc = new MiscDifference(
metadata.Features.MiscDifferences[0].Location);
// Set and validate qualifiers.
miscDiffWithLoc.GeneSymbol = expectedGeneSymbol;
Assert.AreEqual(miscDiffWithLoc.GeneSymbol,
expectedGeneSymbol);
// Log VSTest GUI.
ApplicationLog.WriteLine(
"GenBank Features P1: Successfully validated the GenBank Features");
}
}
