/// <summary>
/// Private constructor for clone method.
/// </summary>
/// <param name="other">Other GCSingal instance.</param>
private GcSingal(GcSingal other)
: base(other)
{
}
/// <summary>
/// Validate GenBank GCSignal features
/// </summary>
/// <param name="nodeName">XML node name</param>
/// <param name="genMetadata">GenBank Metadata</param>
private void ValidateGenBankGCSignalFeature(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<GcSingal> gcSignalFeatureList = genMetadata.Features.GCSignals;
var locBuilder = new LocationBuilder();
// Create a copy of GC_Signal feature.
GcSingal cloneGCSignal = gcSignalFeatureList[0].Clone();
// Validate GC_Signal qualifiers.
Assert.AreEqual(gcSignalFeatureList.Count.ToString((IFormatProvider) null),
featureCount);
Assert.AreEqual(cloneGCSignal.GeneSymbol,
geneSymbol);
Assert.AreEqual(cloneGCSignal.DatabaseCrossReference[0],
expectedDbReference);
Assert.AreEqual(gcSignalFeatureList[0].Allele,
expectedAllele);
Assert.AreEqual(gcSignalFeatureList[0].Citation[0],
expectedCitation);
Assert.AreEqual(gcSignalFeatureList[0].Experiment[0],
expectedExperiment);
Assert.AreEqual(gcSignalFeatureList[0].GenomicMapPosition,
expectedMap);
Assert.AreEqual(gcSignalFeatureList[0].GeneSynonym[0],
expectedGeneSynonym);
Assert.AreEqual(gcSignalFeatureList[0].Inference[0],
expectedInference);
Assert.AreEqual(gcSignalFeatureList[0].Label,
expectedLabel);
Assert.AreEqual(locBuilder.GetLocationString(
genMetadata.Features.GCSignals[0].Location),
expectedLocation);
Assert.AreEqual(gcSignalFeatureList[0].Note[0],
expectedNote);
Assert.AreEqual(gcSignalFeatureList[0].OldLocusTag[0],
expectedOldLocusTag);
Assert.AreEqual(gcSignalFeatureList[0].LocusTag[0],
expectedLocusTag);
// Create a new GCSignal and validate the same.
var gcSignal = new GcSingal(expectedLocation);
var gcSignalWithILoc = new GcSingal(
genMetadata.Features.GCSignals[0].Location);
// Set qualifiers and validate them.
gcSignal.Allele = expectedAllele;
gcSignal.GeneSymbol = geneSymbol;
gcSignalWithILoc.GenomicMapPosition = expectedMap;
Assert.AreEqual(gcSignal.GeneSymbol, geneSymbol);
Assert.AreEqual(gcSignal.Allele, expectedAllele);
Assert.AreEqual(gcSignalWithILoc.GenomicMapPosition,
expectedMap);
}
/// <summary>
/// Private constructor for clone method.
/// </summary>
/// <param name="other">Other GCSingal instance.</param>
private GcSingal(GcSingal other)
: base(other) { }
/// <summary>
/// Validate GenBank Enhancer features
/// </summary>
/// <param name="nodeName">XML node name</param>
/// <param name="genMetadata">GenBank Metadata</param>
private void ValidateGenBankEnhancerFeature(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<Enhancer> enhancerFeatureList = genMetadata.Features.Enhancers;
// Create a copy of Enhancer feature.
Enhancer cloneEnhancer = enhancerFeatureList[0].Clone();
var locBuilder = new LocationBuilder();
// Validate Enhancer qualifiers.
Assert.AreEqual(enhancerFeatureList.Count.ToString((IFormatProvider) null),
featureCount);
Assert.AreEqual(cloneEnhancer.GeneSymbol,
geneSymbol);
Assert.AreEqual(cloneEnhancer.DatabaseCrossReference[0],
expectedDbReference);
Assert.AreEqual(enhancerFeatureList[0].Allele,
expectedAllele);
Assert.AreEqual(enhancerFeatureList[0].Citation[0],
expectedCitation);
Assert.AreEqual(enhancerFeatureList[0].Experiment[0],
expectedExperiment);
Assert.AreEqual(enhancerFeatureList[0].GenomicMapPosition,
expectedMap);
Assert.AreEqual(enhancerFeatureList[0].GeneSynonym[0],
expectedGeneSynonym);
Assert.AreEqual(enhancerFeatureList[0].Inference[0],
expectedInference);
Assert.AreEqual(enhancerFeatureList[0].Label,
expectedLabel);
Assert.AreEqual(locBuilder.GetLocationString(
genMetadata.Features.Enhancers[0].Location),
expectedLocation);
Assert.AreEqual(enhancerFeatureList[0].Note[0],
expectedNote);
Assert.AreEqual(enhancerFeatureList[0].OldLocusTag[0],
expectedOldLocusTag);
Assert.AreEqual(enhancerFeatureList[0].LocusTag[0],
expectedLocusTag);
Assert.IsTrue(string.IsNullOrEmpty(enhancerFeatureList[0].StandardName));
// Create a new Enhancer and validate the same.
var enhancer = new Enhancer(expectedLocation);
var enhancerWithILoc = new GcSingal(
genMetadata.Features.Enhancers[0].Location);
// Set qualifiers and validate them.
enhancer.Allele = expectedAllele;
enhancer.GeneSymbol = geneSymbol;
enhancerWithILoc.GenomicMapPosition = expectedMap;
Assert.AreEqual(enhancer.GeneSymbol, geneSymbol);
Assert.AreEqual(enhancer.Allele, expectedAllele);
Assert.AreEqual(enhancerWithILoc.GenomicMapPosition, expectedMap);
}