/// <summary>
/// Private constructor for clone method.
/// </summary>
/// <param name="other">Other LongTerminalRepeat instance.</param>
private LongTerminalRepeat(LongTerminalRepeat other)
: base(other) { }
/// <summary>
/// Private constructor for clone method.
/// </summary>
/// <param name="other">Other LongTerminalRepeat instance.</param>
private LongTerminalRepeat(LongTerminalRepeat other)
: base(other)
{
}
/// <summary>
/// Validate GenBank LTR features
/// </summary>
/// <param name="nodeName">XML node name</param>
/// <param name="genMetadata">GenBank Metadata</param>
private void ValidateGenBankLTRFeature(string nodeName,
GenBankMetadata genMetadata)
{
// Get Values from XML node.
string expectedLocation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Location);
string expectedAllele = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlleleNode);
string featureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QualifierCount);
string expectedDbReference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DbReferenceNode);
string geneSymbol = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSymbol);
string expectedCitation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CitationNode);
string expectedExperiment = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExperimentNode);
string expectedFunction = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FunctionNode);
string expectedGeneSynonym = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSynonymNode);
string expectedInference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.InferenceNode);
string expectedLabel = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LabelNode);
string expectedLocusTag = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LocusTagNode);
string expectedNote = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Note);
string expectedOldLocusTag = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.OldLocusTagNode);
string expectedMap = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GenbankMapNode);
List<LongTerminalRepeat> LTRFeatureList =
genMetadata.Features.LongTerminalRepeats;
var locBuilder = new LocationBuilder();
// Create a copy of Long Terminal Repeat feature.
LongTerminalRepeat cloneLTR = LTRFeatureList[0].Clone();
// Validate Long Terminal Repeat qualifiers.
Assert.AreEqual(LTRFeatureList.Count.ToString((IFormatProvider) null),
featureCount);
Assert.AreEqual(cloneLTR.GeneSymbol, geneSymbol);
Assert.AreEqual(cloneLTR.DatabaseCrossReference[0],
expectedDbReference);
Assert.AreEqual(LTRFeatureList[0].Allele,
expectedAllele);
Assert.AreEqual(LTRFeatureList[0].Citation[0],
expectedCitation);
Assert.AreEqual(LTRFeatureList[0].Experiment[0],
expectedExperiment);
Assert.AreEqual(LTRFeatureList[0].GenomicMapPosition,
expectedMap);
Assert.AreEqual(LTRFeatureList[0].GeneSynonym[0],
expectedGeneSynonym);
Assert.AreEqual(LTRFeatureList[0].Inference[0],
expectedInference);
Assert.AreEqual(LTRFeatureList[0].Label,
expectedLabel);
Assert.AreEqual(locBuilder.GetLocationString(
genMetadata.Features.LongTerminalRepeats[0].Location),
expectedLocation);
Assert.AreEqual(LTRFeatureList[0].Note[0],
expectedNote);
Assert.AreEqual(LTRFeatureList[0].OldLocusTag[0],
expectedOldLocusTag);
Assert.AreEqual(LTRFeatureList[0].LocusTag[0],
expectedLocusTag);
Assert.AreEqual(LTRFeatureList[0].Function[0],
expectedFunction);
Assert.IsTrue(string.IsNullOrEmpty(LTRFeatureList[0].StandardName));
// Create a new LTR and validate.
var ltr =
new LongTerminalRepeat(expectedLocation);
var ltrWithILoc = new LongTerminalRepeat(
genMetadata.Features.LongTerminalRepeats[0].Location);
// Set qualifiers and validate them.
ltr.Allele = expectedAllele;
ltr.GeneSymbol = geneSymbol;
ltrWithILoc.GenomicMapPosition = expectedMap;
Assert.AreEqual(ltr.GeneSymbol, geneSymbol);
Assert.AreEqual(ltr.Allele, expectedAllele);
Assert.AreEqual(ltrWithILoc.GenomicMapPosition,
expectedMap);
}
