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