/// <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); }