public void InValidateSubSequenceWithComplimentOperator() { // Get Values from XML node. string sequence = utilityObj.xmlUtil.GetTextValue( Constants.InvalidLocationWithComplementOperatorNode, Constants.ExpectedSequence); string location = utilityObj.xmlUtil.GetTextValue( Constants.InvalidLocationWithComplementOperatorNode, Constants.Location); string alphabet = utilityObj.xmlUtil.GetTextValue( Constants.InvalidLocationWithComplementOperatorNode, Constants.AlphabetNameNode); // Create a sequence object. ISequence seqObj = new Sequence(Utility.GetAlphabet(alphabet), sequence); // Build a location. ILocationBuilder locBuilder = new LocationBuilder(); ILocation loc = locBuilder.GetLocation(location); LocationResolver locResolver = new LocationResolver(); // Get sequence using location of the sequence with operator. try { loc.GetSubSequence(seqObj); Assert.Fail(); } catch (ArgumentException) { LogExceptionMessage(); } // Validate sub sequence exception for an invalid sequence. try { locResolver.GetSubSequence(loc, null); Assert.Fail(); } catch (ArgumentNullException) { LogExceptionMessage(); } // Validate GetSubSequence method with null location. try { locResolver.GetSubSequence(null, seqObj); Assert.Fail(); } catch (ArgumentNullException) { LogExceptionMessage(); } // Validate sub sequence exception for an invalid sequence. try { locResolver.GetSubSequence(loc, null, null); Assert.Fail(); } catch (ArgumentNullException) { LogExceptionMessage(); } // Validate GetSubSequence method with null location. try { locResolver.GetSubSequence(null, seqObj, null); Assert.Fail(); } catch (ArgumentNullException) { LogExceptionMessage(); } // Validate GetSubSequence method with null location. try { loc.GetSubSequence(null); Assert.Fail(); } catch (ArgumentNullException) { ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "GenBankFeatures P2 : Validate the exception successfully")); } }
/// <summary> /// InValidate GenBank location with invalid Start location data. /// <param name="endData">Start data used for different test cases.</param> /// </summary> private static void InValidateLocationStartData(string startData) { // Build a location. LocationResolver locResolver = new LocationResolver(); string location = "123.125"; ILocationBuilder locBuilder = new LocationBuilder(); ILocation loc = locBuilder.GetLocation(location); // Set Invalid end data Validate GetStart method exception. loc.StartData = startData; try { locResolver.IsInStart(loc, 124); Assert.Fail(); } catch (IndexOutOfRangeException) { LogExceptionMessage(); } catch (FormatException) { LogExceptionMessage(); } }
public void InValidateGenBankLocationEndData() { // Get Values from XML node. string position = utilityObj.xmlUtil.GetTextValue( Constants.LocationWithEndDataNode, Constants.Position); // Build a location. LocationResolver locResolver = new LocationResolver(); // Validate whether mentioned end data is present in the location // or not. try { locResolver.IsInEnd(null, Int32.Parse(position, (IFormatProvider)null)); Assert.Fail(); } catch (ArgumentNullException) { ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "GenBankFeatures P2 : Validate the exception successfully")); } // Validate IsInStart method exception. try { locResolver.IsInStart(null, Int32.Parse(position, (IFormatProvider)null)); Assert.Fail(); } catch (ArgumentNullException) { LogExceptionMessage(); } // Validate IsInRange method exception. try { locResolver.IsInRange(null, Int32.Parse(position, (IFormatProvider)null)); Assert.Fail(); } catch (ArgumentNullException) { LogExceptionMessage(); } }
public void InValidateGenBankLocationGetStart() { // Build a location. LocationResolver locResolver = new LocationResolver(); // Validate GetStart method exception. try { locResolver.GetStart(null); Assert.Fail(); } catch (ArgumentNullException) { LogExceptionMessage(); } // Validate GetEnd method exception. try { locResolver.GetEnd(null); Assert.Fail(); } catch (ArgumentNullException) { LogExceptionMessage(); } }
/// <summary> /// Default constructor. /// </summary> public Location() { SubLocations = new List <ILocation>(); Resolver = new LocationResolver(); }
/// <summary> /// Default constructor. /// </summary> public Location() { SubLocations = new List<ILocation>(); Resolver = new LocationResolver(); }
/// <summary> /// Validate location resolver end data. /// </summary> /// <param name="nodeName">xml node name.</param> private void ValidateLocationEndData(string nodeName) { // Get Values from XML node. string location = utilityObj.xmlUtil.GetTextValue( nodeName, Constants.Location); string expectedEndData = utilityObj.xmlUtil.GetTextValue( nodeName, Constants.EndData); string position = utilityObj.xmlUtil.GetTextValue( nodeName, Constants.Position); bool result = false; // Build a location. var locResolver = new LocationResolver(); ILocationBuilder locBuilder = new LocationBuilder(); ILocation loc = locBuilder.GetLocation(location); loc.EndData = expectedEndData; // Validate whether mentioned end data is present in the location // or not. result = locResolver.IsInEnd(loc, Int32.Parse(position, null)); Assert.IsTrue(result); // Log to VSTest GUI. ApplicationLog.WriteLine(string.Format(null, "GenBankFeatures P1 : Expected sequence is verified")); }
public void ValidateGenBankLocationStartAndEndRange() { // Get Values from XML node. string filePath = utilityObj.xmlUtil.GetTextValue( Constants.GenBankRepeatRegionQualifiersNode, Constants.FilePathNode); bool startLocResult = false; bool endLocResult = false; bool rangeLocResult = false; // Parse a GenBank file. ISequenceParser parserObj = new GenBankParser(); { ISequence sequence = parserObj.ParseOne(filePath); ILocationResolver locResolver = new LocationResolver(); // Validate Start,End and Range of Gene feature location. var metadata = (GenBankMetadata) sequence.Metadata[Constants.GenBank]; startLocResult = locResolver.IsInStart(metadata.Features.Genes[0].Location, 289); endLocResult = locResolver.IsInEnd(metadata.Features.Genes[0].Location, 1647); rangeLocResult = locResolver.IsInRange(metadata.Features.Genes[0].Location, 300); Assert.IsTrue(startLocResult); Assert.IsTrue(endLocResult); Assert.IsTrue(rangeLocResult); // Log VSTest GUI. ApplicationLog.WriteLine( "GenBank Features P1: Successfully validated the location resolver Gene feature start End and IsInRange methods"); } }
public void ValidateGenBankSubSequence() { // Get Values from XML node. string filePath = utilityObj.xmlUtil.GetTextValue( Constants.GenBankRepeatRegionQualifiersNode, Constants.FilePathNode); string expectedSubSequence = utilityObj.xmlUtil.GetTextValue( Constants.GenBankRepeatRegionQualifiersNode, Constants.ExpectedFeatureSubSequence); // Parse a GenBank file. ISequenceParser parserObj = new GenBankParser(); { ISequence sequence = parserObj.ParseOne(filePath); ILocationResolver locResolver = new LocationResolver(); // Get repeatregion subsequence. var metadata = (GenBankMetadata) sequence.Metadata[Constants.GenBank]; ISequence subSeq = locResolver.GetSubSequence( metadata.Features.RepeatRegions[0].Location, sequence); var sequenceString = new string(subSeq.Select(a => (char) a).ToArray()); // Validate repeat region subsequence. Assert.AreEqual(sequenceString, expectedSubSequence); // Log VSTest GUI. ApplicationLog.WriteLine( "GenBank Features P1: Successfully validated the GenBank subSequence"); } }