/// <summary>
/// Private constructor for clone method.
/// </summary>
/// <param name="other">Other MiscSignal instance.</param>
private MiscSignal(MiscSignal other)
: base(other) { }
/// <summary>
/// Private constructor for clone method.
/// </summary>
/// <param name="other">Other MiscSignal instance.</param>
private MiscSignal(MiscSignal other)
: base(other)
{
}
public void ValidateGenBankMiscSignalFeatureQualifiers()
{
// Get Values from XML node.
string filePath = utilityObj.xmlUtil.GetTextValue(
Constants.GenBankMiscSignalNode, Constants.FilePathNode);
string miscSignalLocation = utilityObj.xmlUtil.GetTextValue(
Constants.GenBankMiscSignalNode, Constants.Location);
string featureCount = utilityObj.xmlUtil.GetTextValue(
Constants.GenBankMiscSignalNode, Constants.QualifierCount);
string geneSymbol = utilityObj.xmlUtil.GetTextValue(
Constants.GenBankMiscSignalNode, Constants.GeneSymbol);
string function = utilityObj.xmlUtil.GetTextValue(
Constants.GenBankMiscSignalNode, Constants.FunctionNode);
string dbReferenceNode = utilityObj.xmlUtil.GetTextValue(
Constants.GenBankMiscSignalNode, Constants.DbReferenceNode);
// 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<MiscSignal> miscSignalList = metadata.Features.MiscSignals;
// Create a clone of MiscSignal feature feature.
MiscSignal cloneMiscSignal = miscSignalList[0].Clone();
Assert.AreEqual(miscSignalList.Count.ToString((IFormatProvider) null), featureCount);
Assert.AreEqual(cloneMiscSignal.GeneSymbol, geneSymbol);
Assert.AreEqual(cloneMiscSignal.DatabaseCrossReference[0], dbReferenceNode);
Assert.IsTrue(string.IsNullOrEmpty(miscSignalList[0].Allele.ToString(null)));
Assert.IsFalse(string.IsNullOrEmpty(miscSignalList[0].Citation.ToString()));
Assert.IsFalse(string.IsNullOrEmpty(miscSignalList[0].Experiment.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(miscSignalList[0].GenomicMapPosition));
Assert.IsFalse(string.IsNullOrEmpty(miscSignalList[0].GeneSynonym.ToString()));
Assert.IsFalse(string.IsNullOrEmpty(miscSignalList[0].Inference.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(miscSignalList[0].Label));
Assert.AreEqual(locBuilder.GetLocationString(
metadata.Features.MiscSignals[0].Location), miscSignalLocation);
Assert.IsFalse(string.IsNullOrEmpty(miscSignalList[0].Note.ToString()));
Assert.IsFalse(string.IsNullOrEmpty(miscSignalList[0].OldLocusTag.ToString()));
Assert.IsFalse(string.IsNullOrEmpty(miscSignalList[0].LocusTag.ToString()));
Assert.AreEqual(miscSignalList[0].Function[0], function);
Assert.IsTrue(string.IsNullOrEmpty(miscSignalList[0].Operon.ToString(null)));
// Create a new MiscSignal signal and validate the same.
var miscSignal = new MiscSignal(miscSignalLocation);
var miscSignalWithIloc = new MiscSignal(
metadata.Features.MiscSignals[0].Location);
// Set qualifiers and validate them.
miscSignal.GeneSymbol = geneSymbol;
miscSignalWithIloc.GeneSymbol = geneSymbol;
Assert.AreEqual(miscSignal.GeneSymbol, geneSymbol);
Assert.AreEqual(miscSignalWithIloc.GeneSymbol, geneSymbol);
// Log VSTest GUI.
ApplicationLog.WriteLine(
"GenBank Features P1: Successfully validated the GenBank Features");
}
}