/// <summary>
/// Private constructor for clone method.
/// </summary>
/// <param name="other">Other ModifiedBase instance.</param>
private ModifiedBase(ModifiedBase other)
: base(other) { }
/// <summary>
/// Private constructor for clone method.
/// </summary>
/// <param name="other">Other ModifiedBase instance.</param>
private ModifiedBase(ModifiedBase other)
: base(other)
{
}
/// <summary>
/// Validate ModifiedBase features
/// </summary>
/// <param name="nodeName">XML node name</param>
/// <param name="genMetadata">GenBank Metadata</param>
private void ValidateGenBankModifiedBaseFeature(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 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<ModifiedBase> modifiedBaseFeatureList =
genMetadata.Features.ModifiedBases;
var locBuilder = new LocationBuilder();
// Create a copy of Modified base feature.
ModifiedBase cloneModifiedBase = modifiedBaseFeatureList[0].Clone();
// Validate Modified Base qualifiers.
Assert.AreEqual(modifiedBaseFeatureList.Count.ToString((IFormatProvider) null),
featureCount);
Assert.AreEqual(cloneModifiedBase.GeneSymbol,
geneSymbol);
Assert.AreEqual(cloneModifiedBase.DatabaseCrossReference[0],
expectedDbReference);
Assert.AreEqual(modifiedBaseFeatureList[0].Allele,
expectedAllele);
Assert.AreEqual(modifiedBaseFeatureList[0].Citation[0],
expectedCitation);
Assert.AreEqual(modifiedBaseFeatureList[0].Experiment[0],
expectedExperiment);
Assert.AreEqual(modifiedBaseFeatureList[0].GenomicMapPosition,
expectedMap);
Assert.AreEqual(modifiedBaseFeatureList[0].GeneSynonym[0],
expectedGeneSynonym);
Assert.AreEqual(modifiedBaseFeatureList[0].Inference[0],
expectedInference);
Assert.AreEqual(modifiedBaseFeatureList[0].Label,
expectedLabel);
Assert.AreEqual(locBuilder.GetLocationString(
genMetadata.Features.ModifiedBases[0].Location),
expectedLocation);
Assert.AreEqual(modifiedBaseFeatureList[0].Note[0],
expectedNote);
Assert.AreEqual(modifiedBaseFeatureList[0].OldLocusTag[0],
expectedOldLocusTag);
Assert.AreEqual(modifiedBaseFeatureList[0].LocusTag[0],
expectedLocusTag);
Assert.IsFalse(string.IsNullOrEmpty(modifiedBaseFeatureList[0].ModifiedNucleotideBase.ToString()));
// Create a new ModifiedBase and validate the same.
var modifiedBase = new ModifiedBase(expectedLocation);
var modifiedBaseWithILoc = new ModifiedBase(
genMetadata.Features.ModifiedBases[0].Location);
// Set qualifiers and validate them.
modifiedBase.Allele = expectedAllele;
modifiedBase.GeneSymbol = geneSymbol;
modifiedBaseWithILoc.GenomicMapPosition = expectedMap;
Assert.AreEqual(modifiedBase.GeneSymbol, geneSymbol);
Assert.AreEqual(modifiedBase.Allele, expectedAllele);
Assert.AreEqual(modifiedBaseWithILoc.GenomicMapPosition,
expectedMap);
}