/// <summary>
/// Private constructor for clone method.
/// </summary>
/// <param name="other">Other MessengerRNA instance.</param>
private MessengerRna(MessengerRna other)
: base(other) { }
/// <summary>
/// Private constructor for clone method.
/// </summary>
/// <param name="other">Other MessengerRNA instance.</param>
private MessengerRna(MessengerRna other)
: base(other)
{
}
/// <summary>
/// Validate GenBank mRNA features.
/// </summary>
/// <param name="nodeName">xml node name.</param>
private void ValidateGenBankmRNAFeatureQualifiers(string nodeName)
{
// Get Values from XML node.
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string mRNAGeneSymbol = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.MRNAGeneSymbol);
string mRNAComplement = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.MRNAComplement);
string mRNADBCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CDSCodonStart);
string mRNAStart = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.MRNAComplementStart);
string mRNAStdName = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.StandardNameNode);
string mRNAAllele = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CDSCodonStart);
string mRNAOperon = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlleleNode);
// Parse a GenBank file.
ISequenceParser parserObj = new GenBankParser();
{
IEnumerable<ISequence> seqList = parserObj.Parse(filePath);
// Validate tRNA feature all qualifiers.
var metadata =
(GenBankMetadata) seqList.ElementAt(0).Metadata[Constants.GenBank];
List<MessengerRna> mRANsList =
metadata.Features.MessengerRNAs;
// Create a copy of mRNA list
MessengerRna mRNAClone = mRANsList[0].Clone();
Assert.AreEqual(mRANsList[0].GeneSymbol.ToString(null),
mRNAGeneSymbol);
Assert.AreEqual(mRANsList[0].DatabaseCrossReference.Count,
Convert.ToInt32(mRNADBCount, null));
Assert.IsTrue(string.IsNullOrEmpty(mRNAClone.Allele));
Assert.IsFalse(string.IsNullOrEmpty(mRANsList[0].Citation.ToString()));
Assert.IsFalse(string.IsNullOrEmpty(mRANsList[0].Experiment.ToString()));
Assert.IsFalse(string.IsNullOrEmpty(mRANsList[0].Function.ToString()));
Assert.IsFalse(string.IsNullOrEmpty(mRANsList[0].GeneSynonym.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(mRANsList[0].GenomicMapPosition));
Assert.IsFalse(string.IsNullOrEmpty(mRANsList[0].Inference.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(mRANsList[0].Label));
Assert.IsFalse(string.IsNullOrEmpty(mRANsList[0].LocusTag.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(mRANsList[0].Operon.ToString(null)));
Assert.IsFalse(string.IsNullOrEmpty(mRANsList[0].Product.ToString()));
Assert.AreEqual(mRANsList[0].Location.Operator.ToString(),
mRNAComplement);
Assert.IsNull(mRANsList[0].Location.Separator);
Assert.AreEqual(mRANsList[0].Location.LocationStart,
Convert.ToInt32(mRNAStart, null));
Assert.IsNull(mRANsList[0].Location.StartData);
Assert.IsNull(mRANsList[0].Location.EndData);
Assert.IsFalse(string.IsNullOrEmpty(mRANsList[0].OldLocusTag.ToString()));
Assert.IsFalse(mRANsList[0].Pseudo);
Assert.IsTrue(string.IsNullOrEmpty(mRANsList[0].StandardName));
Assert.IsFalse(mRANsList[0].TransSplicing);
Assert.IsFalse(string.IsNullOrEmpty(mRANsList[0].LocusTag.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(mRANsList[0].Operon.ToString(null)));
Assert.IsFalse(string.IsNullOrEmpty(mRANsList[0].Product.ToString()));
// Create a new mRNA feature using constructor.
var mRNA = new MessengerRna(
metadata.Features.MessengerRNAs[0].Location);
// Set and validate qualifiers.
mRNA.GeneSymbol = mRNAGeneSymbol;
mRNA.Allele = mRNAAllele;
mRNA.Operon = mRNAOperon;
mRNA.StandardName = mRNAStdName;
// Validate properties.
Assert.AreEqual(mRNA.GeneSymbol, mRNAGeneSymbol);
Assert.AreEqual(mRNA.Allele, mRNAAllele);
Assert.AreEqual(mRNA.Operon, mRNAOperon);
Assert.AreEqual(mRNA.StandardName, mRNAStdName);
// Log VSTest GUI.
ApplicationLog.WriteLine(
"GenBank Features P1: Successfully validated the GenBank Features");
}
}
