/// <summary>
/// Private constructor for clone method.
/// </summary>
/// <param name="other">Other DisplacementLoop instance.</param>
private DisplacementLoop(DisplacementLoop other)
: base(other) { }
/// <summary>
/// Private constructor for clone method.
/// </summary>
/// <param name="other">Other DisplacementLoop instance.</param>
private DisplacementLoop(DisplacementLoop other)
: base(other)
{
}
public void ValidateGenBankDLoopFeatureQualifiers()
{
// Get Values from XML node.
string filePath = utilityObj.xmlUtil.GetTextValue(
Constants.GenBankDLoopNode, Constants.FilePathNode);
string dLoopLocation = utilityObj.xmlUtil.GetTextValue(
Constants.GenBankDLoopNode, Constants.Location);
string featureCount = utilityObj.xmlUtil.GetTextValue(
Constants.GenBankDLoopNode, Constants.QualifierCount);
string geneSymbol = utilityObj.xmlUtil.GetTextValue(
Constants.GenBankDLoopNode, 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<DisplacementLoop> dLoopList = metadata.Features.DisplacementLoops;
// Create a clone of DLoop feature feature.
DisplacementLoop cloneDLoop = dLoopList[0].Clone();
Assert.AreEqual(dLoopList.Count.ToString((IFormatProvider) null), featureCount);
Assert.AreEqual(cloneDLoop.GeneSymbol, geneSymbol);
Assert.IsFalse(string.IsNullOrEmpty(cloneDLoop.DatabaseCrossReference.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(dLoopList[0].Allele.ToString(null)));
Assert.IsFalse(string.IsNullOrEmpty(dLoopList[0].Citation.ToString()));
Assert.IsFalse(string.IsNullOrEmpty(dLoopList[0].Experiment.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(dLoopList[0].GenomicMapPosition));
Assert.IsFalse(string.IsNullOrEmpty(dLoopList[0].GeneSynonym.ToString()));
Assert.IsFalse(string.IsNullOrEmpty(dLoopList[0].Inference.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(dLoopList[0].Label));
Assert.AreEqual(locBuilder.GetLocationString(
metadata.Features.DisplacementLoops[0].Location), dLoopLocation);
Assert.IsFalse(string.IsNullOrEmpty(dLoopList[0].Note.ToString()));
Assert.IsFalse(string.IsNullOrEmpty(dLoopList[0].OldLocusTag.ToString()));
Assert.IsFalse(string.IsNullOrEmpty(dLoopList[0].LocusTag.ToString()));
Assert.IsFalse(string.IsNullOrEmpty(dLoopList[0].OldLocusTag.ToString()));
// Create a new DLoop signal and validate the same.
var dLoop = new DisplacementLoop(dLoopLocation);
var dLoopWithIloc = new DisplacementLoop(
metadata.Features.DisplacementLoops[0].Location);
// Set qualifiers and validate them.
dLoop.GeneSymbol = geneSymbol;
dLoopWithIloc.GeneSymbol = geneSymbol;
Assert.AreEqual(dLoop.GeneSymbol, geneSymbol);
Assert.AreEqual(dLoopWithIloc.GeneSymbol, geneSymbol);
// Log VSTest GUI.
ApplicationLog.WriteLine(
"GenBank Features P1: Successfully validated the GenBank Features");
}
}
