/// <summary>
/// Private constructor for clone method.
/// </summary>
/// <param name="other">Other CodingSequence instance.</param>
private CodingSequence(CodingSequence other)
: base(other) { }
/// <summary>
/// Private constructor for clone method.
/// </summary>
/// <param name="other">Other CodingSequence instance.</param>
private CodingSequence(CodingSequence other)
: base(other)
{
}
/// <summary>
/// Validate GenBank CDS features
/// </summary>
/// <param name="nodeName">XML node name</param>
/// <param name="genMetadata">GenBank Metadata</param>
private void ValidateGenBankCDSFeatures(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 expectedInference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.InferenceNode);
string expectedLabel = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LabelNode);
string expectedNote = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Note);
string expectedMap = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GenbankMapNode);
string expectedTranslation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GenbankTranslationNode);
string expectedCodonStart = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CodonStartNode);
List<CodingSequence> codingSequenceFeatureList =
genMetadata.Features.CodingSequences;
var locBuilder = new LocationBuilder();
// Create a copy of Coding Seq Region feature.
CodingSequence cloneCDS = codingSequenceFeatureList[0].Clone();
// Validate Unsure Seq Region qualifiers.
Assert.AreEqual(codingSequenceFeatureList.Count.ToString((IFormatProvider) null),
featureCount);
Assert.AreEqual(cloneCDS.DatabaseCrossReference[0],
expectedDbReference);
Assert.AreEqual(cloneCDS.GeneSymbol, geneSymbol);
Assert.AreEqual(codingSequenceFeatureList[0].Allele,
expectedAllele);
Assert.AreEqual(codingSequenceFeatureList[0].Citation[0],
expectedCitation);
Assert.AreEqual(codingSequenceFeatureList[0].Experiment[0],
expectedExperiment);
Assert.AreEqual(codingSequenceFeatureList[0].GenomicMapPosition,
expectedMap);
Assert.AreEqual(codingSequenceFeatureList[0].Inference[0],
expectedInference);
Assert.AreEqual(codingSequenceFeatureList[0].Label,
expectedLabel);
Assert.AreEqual(locBuilder.GetLocationString(
genMetadata.Features.CodingSequences[0].Location),
expectedLocation);
Assert.AreEqual(codingSequenceFeatureList[0].Note[0],
expectedNote);
Assert.AreEqual(codingSequenceFeatureList[0].GenomicMapPosition,
expectedMap);
Assert.AreEqual(codingSequenceFeatureList[0].CodonStart[0],
expectedCodonStart);
Assert.AreEqual(codingSequenceFeatureList[0].Translation,
expectedTranslation);
Assert.IsFalse(string.IsNullOrEmpty(codingSequenceFeatureList[0].Codon.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(codingSequenceFeatureList[0].EnzymeCommissionNumber));
Assert.IsTrue(string.IsNullOrEmpty(codingSequenceFeatureList[0].Number));
Assert.IsTrue(string.IsNullOrEmpty(codingSequenceFeatureList[0].Operon));
Assert.IsFalse(codingSequenceFeatureList[0].Pseudo);
Assert.IsFalse(codingSequenceFeatureList[0].RibosomalSlippage);
Assert.IsTrue(string.IsNullOrEmpty(codingSequenceFeatureList[0].StandardName));
Assert.IsFalse(string.IsNullOrEmpty(codingSequenceFeatureList[0].TranslationalExcept.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(codingSequenceFeatureList[0].TranslationTable));
Assert.IsFalse(codingSequenceFeatureList[0].TransSplicing);
Assert.IsTrue(string.IsNullOrEmpty(codingSequenceFeatureList[0].Exception));
// Create a new CDS feature using constructor.
var cds = new CodingSequence(expectedLocation);
var cdsWithLoc = new CodingSequence(
genMetadata.Features.CodingSequences[0].Location);
Sequence seq = cds.GetTranslation();
Assert.IsNotNull(seq);
// Set and validate qualifiers.
cds.Allele = expectedAllele;
cdsWithLoc.GeneSymbol = geneSymbol;
cdsWithLoc.GenomicMapPosition = expectedMap;
Assert.AreEqual(cdsWithLoc.GenomicMapPosition, expectedMap);
Assert.AreEqual(cds.Allele, expectedAllele);
Assert.AreEqual(cdsWithLoc.GeneSymbol, geneSymbol);
}
