Exemple #1
0
 /// <summary>
 /// Private constructor for clone method.
 /// </summary>
 /// <param name="other">Other Terminator instance.</param>
 private Terminator(Terminator other)
     : base(other) { }
Exemple #2
0
 /// <summary>
 /// Private constructor for clone method.
 /// </summary>
 /// <param name="other">Other Terminator instance.</param>
 private Terminator(Terminator other)
     : base(other)
 {
 }
        public void ValidateGenBankTerminatorFeatureQualifiers()
        {
            // Get Values from XML node.
            string filePath = utilityObj.xmlUtil.GetTextValue(
                Constants.GenBankTerminatorNode, Constants.FilePathNode);
            string terminatorLocation = utilityObj.xmlUtil.GetTextValue(
                Constants.GenBankTerminatorNode, Constants.Location);
            string featureCount = utilityObj.xmlUtil.GetTextValue(
                Constants.GenBankTerminatorNode, Constants.QualifierCount);
            string geneSymbol = utilityObj.xmlUtil.GetTextValue(
                Constants.GenBankTerminatorNode, Constants.GeneSymbol);

            // Parse a GenBank file.
            ISequenceParser parserObj = new GenBankParser();
            {
                IEnumerable<ISequence> seqList = parserObj.Parse(filePath);
                var locBuilder = new LocationBuilder();

                var metadata =
                    (GenBankMetadata) seqList.ElementAt(0).Metadata[Constants.GenBank];
                List<Terminator> terminatorList = metadata.Features.Terminators;

                // Create a clone of Terminator feature feature.
                Terminator cloneTerminator = terminatorList[0].Clone();
                Assert.AreEqual(terminatorList.Count.ToString((IFormatProvider) null), featureCount);
                Assert.AreEqual(cloneTerminator.GeneSymbol, geneSymbol);
                Assert.IsFalse(string.IsNullOrEmpty(cloneTerminator.DatabaseCrossReference.ToString()));
                Assert.IsTrue(string.IsNullOrEmpty(terminatorList[0].Allele));
                Assert.IsFalse(string.IsNullOrEmpty(terminatorList[0].Citation.ToString()));
                Assert.IsFalse(string.IsNullOrEmpty(terminatorList[0].Experiment.ToString()));
                Assert.IsTrue(string.IsNullOrEmpty(terminatorList[0].GenomicMapPosition));
                Assert.IsFalse(string.IsNullOrEmpty(terminatorList[0].GeneSynonym.ToString()));
                Assert.IsFalse(string.IsNullOrEmpty(terminatorList[0].Inference.ToString()));
                Assert.IsTrue(string.IsNullOrEmpty(terminatorList[0].Label));
                Assert.AreEqual(locBuilder.GetLocationString(
                    metadata.Features.Terminators[0].Location), terminatorLocation);
                Assert.IsFalse(string.IsNullOrEmpty(terminatorList[0].Note.ToString()));
                Assert.IsFalse(string.IsNullOrEmpty(terminatorList[0].OldLocusTag.ToString()));
                Assert.IsFalse(string.IsNullOrEmpty(terminatorList[0].LocusTag.ToString()));
                Assert.IsTrue(string.IsNullOrEmpty(terminatorList[0].StandardName));

                // Create a new Terminator signal and validate the same.
                var terminator = new Terminator(terminatorLocation);
                var terminatorWithILoc = new Terminator(
                    metadata.Features.Terminators[0].Location);

                // Set qualifiers and validate them.
                terminator.GeneSymbol = geneSymbol;
                terminatorWithILoc.GeneSymbol = geneSymbol;
                Assert.AreEqual(terminator.GeneSymbol, geneSymbol);
                Assert.AreEqual(terminatorWithILoc.GeneSymbol, geneSymbol);

                // Log VSTest GUI.
                ApplicationLog.WriteLine(
                    "GenBank Features P1: Successfully validated the GenBank Features");
            }
        }