/// <summary>
/// Private constructor for clone method.
/// </summary>
/// <param name="other">Other PolyASignal instance.</param>
private PolyASignal(PolyASignal other)
: base(other) { }
/// <summary>
/// Private constructor for clone method.
/// </summary>
/// <param name="other">Other PolyASignal instance.</param>
private PolyASignal(PolyASignal other)
: base(other)
{
}
public void ValidateGenBankPolyASignalFeatureQualifiers()
{
// Get Values from XML node.
string filePath = utilityObj.xmlUtil.GetTextValue(
Constants.GenBankPolyASignalNode, Constants.FilePathNode);
string polyALocation = utilityObj.xmlUtil.GetTextValue(
Constants.GenBankPolyASignalNode, Constants.Location);
string featureCount = utilityObj.xmlUtil.GetTextValue(
Constants.GenBankPolyASignalNode, Constants.QualifierCount);
string geneSymbol = utilityObj.xmlUtil.GetTextValue(
Constants.GenBankPolyASignalNode, Constants.GeneSymbol);
// Parse a GenBank file.
ISequenceParser parserObj = new GenBankParser();
{
IEnumerable<ISequence> seqList = parserObj.Parse(filePath);
var locBuilder = new LocationBuilder();
// Validate Minus35Signal feature all qualifiers.
var metadata =
(GenBankMetadata) seqList.ElementAt(0).Metadata[Constants.GenBank];
List<PolyASignal> polyASignalList = metadata.Features.PolyASignals;
// Create a clone of PolyASignal feature feature.
PolyASignal cloneMinus10Signal = polyASignalList[0].Clone();
Assert.AreEqual(polyASignalList.Count.ToString((IFormatProvider) null), featureCount);
Assert.AreEqual(cloneMinus10Signal.GeneSymbol, geneSymbol);
Assert.IsFalse(string.IsNullOrEmpty(cloneMinus10Signal.DatabaseCrossReference.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(polyASignalList[0].Allele));
Assert.IsFalse(string.IsNullOrEmpty(polyASignalList[0].Citation.ToString()));
Assert.IsFalse(string.IsNullOrEmpty(polyASignalList[0].Experiment.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(polyASignalList[0].GenomicMapPosition));
Assert.IsFalse(string.IsNullOrEmpty(polyASignalList[0].GeneSynonym.ToString()));
Assert.IsFalse(string.IsNullOrEmpty(polyASignalList[0].Inference.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(polyASignalList[0].Label));
Assert.AreEqual(locBuilder.GetLocationString(
metadata.Features.PolyASignals[0].Location), polyALocation);
Assert.IsFalse(string.IsNullOrEmpty(polyASignalList[0].Note.ToString()));
Assert.IsFalse(string.IsNullOrEmpty(polyASignalList[0].OldLocusTag.ToString()));
Assert.IsFalse(string.IsNullOrEmpty(polyASignalList[0].LocusTag.ToString()));
// Create a new PolyA signal and validate the same.
var polyASignal = new PolyASignal(polyALocation);
var polyASignalWithILoc = new PolyASignal(
metadata.Features.Minus10Signals[0].Location);
// Set qualifiers and validate them.
polyASignal.GeneSymbol = geneSymbol;
polyASignalWithILoc.GeneSymbol = geneSymbol;
Assert.AreEqual(polyASignal.GeneSymbol, geneSymbol);
Assert.AreEqual(polyASignalWithILoc.GeneSymbol, geneSymbol);
// Log VSTest GUI.
ApplicationLog.WriteLine(
"GenBank Features P1: Successfully validated the GenBank Features");
}
}
