Exemple #1
0
 /// <summary>
 /// Private constructor for clone method.
 /// </summary>
 /// <param name="other">Other MiscDifference instance.</param>
 private MiscDifference(MiscDifference other)
     : base(other) { }
Exemple #2
0
 /// <summary>
 /// Private constructor for clone method.
 /// </summary>
 /// <param name="other">Other MiscDifference instance.</param>
 private MiscDifference(MiscDifference other)
     : base(other)
 {
 }
        /// <summary>
        ///     Validate GenBank Misc difference feature qualifiers.
        /// </summary>
        /// <param name="nodeName">xml node name.</param>
        private void ValidateGenBankMiscDiffFeatureQualifiers(string nodeName)
        {
            // Get Values from XML node.
            string filePath = utilityObj.xmlUtil.GetTextValue(
                nodeName, Constants.FilePathNode);
            string expectedMiscDiffCount = utilityObj.xmlUtil.GetTextValue(
                nodeName, Constants.MiscDiffCount);
            string expectedGeneSymbol = utilityObj.xmlUtil.GetTextValue(
                nodeName, Constants.GeneSymbol);

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

                // Validate Protein feature all qualifiers.
                var metadata =
                    (GenBankMetadata) seqList.ElementAt(1).Metadata[Constants.GenBank];
                List<MiscDifference> miscDifferenceFeatureList =
                    metadata.Features.MiscDifferences;
                Assert.AreEqual(miscDifferenceFeatureList.Count.ToString((IFormatProvider) null),
                                expectedMiscDiffCount);
                Assert.AreEqual(miscDifferenceFeatureList[0].GeneSymbol,
                                expectedGeneSymbol);
                Assert.IsTrue(string.IsNullOrEmpty(miscDifferenceFeatureList[0].Allele));
                Assert.IsFalse(string.IsNullOrEmpty(miscDifferenceFeatureList[0].Citation.ToString()));
                Assert.IsFalse(string.IsNullOrEmpty(miscDifferenceFeatureList[0].Experiment.ToString()));
                Assert.IsFalse(string.IsNullOrEmpty(miscDifferenceFeatureList[0].GeneSynonym.ToString()));
                Assert.IsTrue(string.IsNullOrEmpty(miscDifferenceFeatureList[0].GenomicMapPosition));
                Assert.IsFalse(string.IsNullOrEmpty(miscDifferenceFeatureList[0].Inference.ToString()));
                Assert.IsTrue(string.IsNullOrEmpty(miscDifferenceFeatureList[0].Label));
                Assert.IsFalse(string.IsNullOrEmpty(miscDifferenceFeatureList[0].OldLocusTag.ToString()));
                Assert.IsTrue(string.IsNullOrEmpty(miscDifferenceFeatureList[0].StandardName));
                Assert.IsTrue(string.IsNullOrEmpty(miscDifferenceFeatureList[0].Replace));
                Assert.IsFalse(string.IsNullOrEmpty(miscDifferenceFeatureList[0].Phenotype.ToString()));
                Assert.IsFalse(string.IsNullOrEmpty(miscDifferenceFeatureList[0].OldLocusTag.ToString()));
                Assert.IsFalse(string.IsNullOrEmpty(miscDifferenceFeatureList[0].LocusTag.ToString()));
                Assert.IsFalse(string.IsNullOrEmpty(miscDifferenceFeatureList[0].Compare.ToString()));
                Assert.IsFalse(string.IsNullOrEmpty(miscDifferenceFeatureList[0].DatabaseCrossReference.ToString()));
                Assert.IsTrue(string.IsNullOrEmpty(miscDifferenceFeatureList[0].ClonedFrom));


                // Create a new MiscDiff feature using constructor.
                var miscDiffWithLoc = new MiscDifference(
                    metadata.Features.MiscDifferences[0].Location);

                // Set and validate qualifiers.
                miscDiffWithLoc.GeneSymbol = expectedGeneSymbol;
                Assert.AreEqual(miscDiffWithLoc.GeneSymbol,
                                expectedGeneSymbol);

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