public void InvalidateBioHPCBlastHandler() { try { IBlastServiceHandler handler = new BioHPCBlastHandler(null, new ConfigParameters()); Assert.Fail(); } catch (ArgumentNullException anex) { ApplicationLog.WriteLine("Successfully caught ArgumentNullException : " + anex.Message); } try { IBlastParser blastXmlParser = new BlastXmlParser(); IBlastServiceHandler handler = new BioHPCBlastHandler(blastXmlParser, null); Assert.Fail(); } catch (ArgumentNullException anex) { ApplicationLog.WriteLine("Successfully caught ArgumentNullException : " + anex.Message); } }
/// <summary> /// Creates a sparse sequence and inserts sequence items of alphabet. /// Creates copy of sparse sequence object using clone() method. /// and Validates if copy of sparse sequence is as expected. /// </summary> /// <param name="alphabet">alphabet instance.</param> private void ValidateSparseSequenceCopy(IAlphabet alphabet) { SparseSequence sparseSequence = CreateSparseSequence(alphabet, 15); SparseSequence sparseSeqCopy = sparseSequence.Clone(); // Retrieve all stored sequence items and validate Sparse Sequence int retrieveIndex = 15; foreach (ISequenceItem item in alphabet) { // Validate new added items Assert.IsTrue(sparseSeqCopy.Contains(item)); Assert.AreEqual(sparseSeqCopy.IndexOf(item), retrieveIndex); Assert.AreEqual(item, sparseSeqCopy[retrieveIndex]); Assert.AreEqual(item.Symbol, sparseSeqCopy[retrieveIndex].Symbol); retrieveIndex++; } Console.WriteLine( "SparseSequenceBVT: Validation of copy of sparse sequence object is completed"); ApplicationLog.WriteLine( "SparseSequenceBVT: Validation of copy of sparse sequence object is completed"); }
public void ValidateMoreThanTwelveCharsDnaComplementation() { // Get Node values from XML. string alphabetName = utilityObj.xmlUtil.GetTextValue( Constants.SimpleDnaAlphabetNode, Constants.AlphabetNameNode); string expectedSeq = utilityObj.xmlUtil.GetTextValue( Constants.ComplementNode, Constants.DnaSymbol); string expectedComplement = utilityObj.xmlUtil.GetTextValue( Constants.ComplementNode, Constants.DnaSymbolComplement); ISequence complement = null; Sequence seq = new Sequence(Utility.GetAlphabet(alphabetName), expectedSeq); // Complement DNA Sequence. complement = seq.GetComplementedSequence(); // Validate Complement for a given sequence. Assert.AreEqual(new string(complement.Select(a => (char)a).ToArray()), expectedComplement); ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "Translation P1: Complement {0} is expected.", complement)); ApplicationLog.WriteLine( "Translation P1: Complement of More than twelve DNA characters sequence was validate successfully."); }
public void ValidateDnaComplementation() { // Get Node values from XML. string alphabetName = this.utilityObj.xmlUtil.GetTextValue( Constants.SimpleDnaAlphabetNode, Constants.AlphabetNameNode); string expectedSeq = this.utilityObj.xmlUtil.GetTextValue( Constants.ComplementNode, Constants.DnaSequence); string expectedComplement = this.utilityObj.xmlUtil.GetTextValue( Constants.ComplementNode, Constants.DnaComplement); ISequence complement = null; var seq = new Sequence(Utility.GetAlphabet(alphabetName), expectedSeq); // Complement DNA Sequence. complement = seq.GetComplementedSequence(); // Validate Complement. Assert.AreEqual(new string(complement.Select(a => (char)a).ToArray()), expectedComplement); ApplicationLog.WriteLine(string.Format(null, "Translation BVT: Complement {0} is expected.", seq)); ApplicationLog.WriteLine( "Translation BVT: Complement of DNA sequence was validate successfully."); }
public void ValidateRnaSparseSequenceConstAlpIndexByteList() { byte[] byteArrayObj = Encoding.ASCII.GetBytes("AGCU"); IEnumerable <byte> seqItems = new List <Byte> { byteArrayObj[0], byteArrayObj[1], byteArrayObj[2], byteArrayObj[3] }; var sparseSeq = new SparseSequence(Alphabets.RNA, 4, seqItems); Assert.IsNotNull(sparseSeq); Assert.IsNotNull(sparseSeq.Statistics); Assert.AreEqual(8, sparseSeq.Count); SequenceStatistics seqStatObj = sparseSeq.Statistics; Assert.AreEqual(1, seqStatObj.GetCount('A')); Assert.AreEqual(1, seqStatObj.GetCount('G')); Assert.AreEqual(1, seqStatObj.GetCount('C')); Assert.AreEqual(1, seqStatObj.GetCount('U')); ApplicationLog.WriteLine("SparseSequence P1: Validation of SparseSequence(alp, index, seq items) constructor is completed"); }
public void ValidateOperatorOutputFile() { OutputFile outputFile = null; string filename = Path.GetTempFileName(); using (File.Create(filename)) { }; FileInfo fileinfo = new FileInfo(filename); try { outputFile = fileinfo; Assert.IsNotNull(outputFile, "OutputFile BVT: OutputFile Operator OutputFile Validated successfully"); fileinfo = null; outputFile = fileinfo; Assert.IsNull(outputFile, "OutputFile BVT: OutputFile Operator OutputFile Validated successfully"); } catch (Exception ex) { ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "OutputFile BVT: OutputFile OutputFile not validated successfully:", ex.Message)); Assert.Fail("OutputFile BVT: OutputFile OutputFile not validated successfully"); } }
public void ValidateMoreThanTwelveCharsDnaReverseTranscribe() { // Get Node values from XML. string alphabetName = _utilityObj._xmlUtil.GetTextValue( Constants.SimpleDnaAlphabetNode, Constants.AlphabetNameNode); string expectedSeq = _utilityObj._xmlUtil.GetTextValue( Constants.ComplementNode, Constants.DnaSequenceWithMoreThanTwelveChars); string expectedTranscribe = _utilityObj._xmlUtil.GetTextValue( Constants.TranscribeNode, Constants.DnaRevTranscribeForMoreThanTwelveChars); ISequence seq = new Sequence(Utility.GetAlphabet(alphabetName), expectedSeq); // Reverse Transcribe DNA Sequence. ISequence transcribe = Transcription.Transcribe(seq); ISequence revTranscribe = Transcription.ReverseTranscribe(transcribe); // Validate reverse transcribe.for a given sequence. Assert.AreEqual(revTranscribe.ToString(), expectedTranscribe); ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "Translation P1: Reverse Transcribe {0} is expected.", revTranscribe)); ApplicationLog.WriteLine( "Translation P1: Reverse Transcribe of Single DNA Symbol was validate successfully."); }
/// <summary> /// Validate sequence alignment instance using different aligners /// </summary> /// <param name="nodeName">xml node name</param> /// <param name="aligner">sw/nw/pw aligners</param> private void ValidateSequenceAlignment(string nodeName, ISequenceAligner aligner) { IAlphabet alphabet = Utility.GetAlphabet(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.AlphabetNameNode)); string origSequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceNode1); string origSequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceNode2); // Create input sequences var inputSequences = new List <ISequence>(); inputSequences.Add(new Sequence(alphabet, origSequence1)); inputSequences.Add(new Sequence(alphabet, origSequence2)); // Get aligned sequences IList <ISequenceAlignment> alignments = aligner.Align(inputSequences); ISequenceAlignment alignment = alignments[0]; Assert.AreEqual(alignments[0].AlignedSequences.Count, alignment.AlignedSequences.Count); Assert.AreEqual(alignments[0].Metadata, alignment.Metadata); Assert.AreEqual(inputSequences[0].ToString(), alignment.Sequences[0].ToString()); ApplicationLog.WriteLine(@"Alignment BVT : Validation of sequence alignment completed successfully"); }
public void ValidateReadOnlyAlignedSeqGetIEnumerable() { string filePath = Utility._xmlUtil.GetTextValue(Constants.SAMFileWithAllFieldsNode, Constants.FilePathNode); SAMParser samParserObj = new SAMParser(); samParserObj.EnforceDataVirtualization = true; SequenceAlignmentMap alignedSeqList = samParserObj.Parse(filePath); IList <SAMAlignedSequence> samAlignedList = alignedSeqList.QuerySequences; IEnumerable readOnlyCollections = new ReadOnlyAlignedSequenceCollection(samAlignedList); IEnumerator enumerator = readOnlyCollections.GetEnumerator(); Assert.IsNotNull(enumerator); ApplicationLog.WriteLine(string.Format(null, "ReadOnlyAlignedSeqCollection P1 : Validated the ReadOnlyAlignedSeq GetEnumerator")); Console.WriteLine(string.Format(null, "ReadOnlyAlignedSeqCollection P1 : Validated the ReadOnlyAlignedSeq GetEnumerator")); }
public void ValidateSingleSymbolDnaReverseTranscribe() { // Get Node values from XML. string alphabetName = Utility._xmlUtil.GetTextValue( Constants.SimpleDnaAlphabetNode, Constants.AlphabetNameNode); string expectedSeq = Utility._xmlUtil.GetTextValue( Constants.TranscribeNode, Constants.DnaSymbol); string expectedTranscribe = Utility._xmlUtil.GetTextValue( Constants.TranscribeNode, Constants.DnaSymbolRevTranscribe); ISequence seq = new Sequence(Utility.GetAlphabet(alphabetName), expectedSeq); // Reverse Transcribe DNA Symbol. ISequence transcribe = Transcription.Transcribe(seq); ISequence revTranscribe = Transcription.ReverseTranscribe(transcribe); // Validate Single DNA Symbol Reverse transcribe. Assert.AreEqual(revTranscribe.ToString(), expectedTranscribe); ApplicationLog.WriteLine(string.Format(null, "Translation P1: Reverse Transcribe {0} is expected.", revTranscribe)); ApplicationLog.WriteLine( "Translation P1: Reverse Transcribe of Single DNA Symbol was validate successfully."); }
public void InvalidateParseForNullArgumentsNo() { CommandLineArguments parser = new CommandLineArguments(); //add parameters parser.Parameter(ArgumentType.Required, "InputFile", ArgumentValueType.String, "i", "File containing numbers to add"); parser.Parameter(ArgumentType.Required, "ResultFile", ArgumentValueType.String, "r", "File to store output"); string inputfileName = Path.GetTempFileName().Replace(Path.GetTempPath(), ""); string outputfileName = Path.GetTempFileName().Replace(Path.GetTempPath(), ""); string[] args = { "/InputFile:" + inputfileName, "/ResultFile:" + outputfileName }; try { parser.Parse(args, null); Assert.Fail("CommandLineArguments P2: Not validated parameter Method for null value"); } catch (ArgumentNullException ex) { ApplicationLog.WriteLine("CommandLineArguments P2: Successfully validated Parameter Method for null value:", ex.Message); } }
public void ValidateDnaDerivedSequenceProperties() { // Get input and expected values from xml string expectedSequence = utilityObj.xmlUtil.GetTextValue( Constants.DnaDerivedSequenceNode, Constants.ExpectedSequence); string alphabetName = utilityObj.xmlUtil.GetTextValue( Constants.DnaDerivedSequenceNode, Constants.AlphabetNameNode); string derivedSequence = utilityObj.xmlUtil.GetTextValue( Constants.DnaDerivedSequenceNode, Constants.DerivedSequence); IAlphabet alphabet = Utility.GetAlphabet(alphabetName); // Create derived Sequence DerivedSequence derSequence = CreateDerivedSequence( alphabet, expectedSequence); // Validate properties of derived Sequence. Assert.AreEqual(derivedSequence, new string(derSequence.Select(a => (char)a).ToArray())); Assert.AreEqual(alphabet, derSequence.Alphabet); Assert.IsNotNull(derSequence.Metadata); ApplicationLog.WriteLine( "DerivedSequenceBvtTestCases:Validation of properties of derived sequence completed successfully"); }
public void ValidateCompareTwoSequenceRanges() { // Get values from xml. string expectedRangeId = this.utilityObj.xmlUtil.GetTextValue(Constants.SequenceRangeNode, Constants.IDNode); string expectedStartIndex = this.utilityObj.xmlUtil.GetTextValue(Constants.SequenceRangeNode, Constants.StartNode); string expectedEndIndex = this.utilityObj.xmlUtil.GetTextValue(Constants.SequenceRangeNode, Constants.EndNode); string expectedRangeId1 = this.utilityObj.xmlUtil.GetTextValue(Constants.SequenceRangeNode, Constants.IDNode1); string expectedStartIndex1 = this.utilityObj.xmlUtil.GetTextValue(Constants.SequenceRangeNode, Constants.StartNode1); string expectedEndIndex1 = this.utilityObj.xmlUtil.GetTextValue(Constants.SequenceRangeNode, Constants.EndNode1); // Create first SequenceRange. var seqRange = new SequenceRange(expectedRangeId, long.Parse(expectedStartIndex, null), long.Parse(expectedEndIndex, null)); // Create second SequenceRange. var secondSeqRange = new SequenceRange(expectedRangeId1, long.Parse(expectedStartIndex1, null), long.Parse(expectedEndIndex1, null)); // Compare two SequenceRanges which are identical. int result = seqRange.CompareTo(secondSeqRange); // Validate result of comparison. Assert.AreEqual(0, result); ApplicationLog.WriteLine("SequenceRange BVT : Successfully validated the SequenceRange comparison"); }
public void ValidateDensePairAnsiWriteDensePairAnsi() { List <KeyValuePair <string, UOPair <char> > > keyValListObj = new List <KeyValuePair <string, UOPair <char> > >(); var enumObj = keyValListObj.GroupBy(x => x.Key); DensePairAnsi dpaObj = DensePairAnsi.GetInstance(enumObj, '?'); ParallelOptions paObj = new ParallelOptions(); dpaObj.WriteDensePairAnsi(Constants.FastQTempTxtFileName, paObj); DensePairAnsi newDpaObj = DensePairAnsi.GetInstance(Constants.FastQTempTxtFileName, paObj); Assert.IsNotNull(newDpaObj); Console.WriteLine( "DensePairAnsi BVT : Validation of WriteDensePairAnsi() method successful"); ApplicationLog.WriteLine( "DensePairAnsi BVT : Validation of WriteDensePairAnsi() method successful"); }
/// <summary> /// Validates general Parse test cases with Fasta parser object name specified. /// </summary> /// <param name="parserObj">fasta parser object.</param> private void ValidateParserGeneralTestCases(FastAParser parserObj) { IList <ISequence> seqs = parserObj.Parse().ToList(); Assert.AreEqual(1, seqs.Count); ApplicationLog.WriteLine("FastA Parser with Alphabet: Number of Sequences found are '{0}'.", seqs.Count); // Gets the expected sequence from the Xml string expectedSequence = utilityObj.xmlUtil.GetTextValue(Constants.SimpleFastaDnaNodeName, Constants.ExpectedSequenceNode); string newSequence = seqs[0].ConvertToString(); Assert.AreEqual(expectedSequence, newSequence); ISequence seq = seqs[0]; var tmpEncodedSeq = new byte[seq.Count]; seq.ToArray().CopyTo(tmpEncodedSeq, 0); Assert.AreEqual(expectedSequence.Length, tmpEncodedSeq.Length); Assert.IsNotNull(seq.Alphabet); Assert.AreEqual(seq.Alphabet.Name.ToLower(CultureInfo.CurrentCulture), utilityObj.xmlUtil.GetTextValue(Constants.SimpleFastaDnaNodeName, Constants.AlphabetNameNode).ToLower(CultureInfo.CurrentCulture)); Assert.AreEqual(utilityObj.xmlUtil.GetTextValue(Constants.SimpleFastaDnaNodeName, Constants.SequenceIdNode), seq.ID); }
public void ValidateLookupWithZeroOffset() { string alphabetName = Utility._xmlUtil.GetTextValue(Constants.SimpleRnaAlphabetNode, Constants.AlphabetNameNode); string expectedSeq = Utility._xmlUtil.GetTextValue(Constants.CodonsNode, Constants.SequenceWithmoreThanTweleveChars); string expectedAminoAcid = Utility._xmlUtil.GetTextValue(Constants.CodonsNode, Constants.OffsetOneMoreThanTwelveCharsAminoAcid); string expectedOffset = Utility._xmlUtil.GetTextValue(Constants.CodonsNode, Constants.OffsetVaule4); ISequence seq = new Sequence(Utility.GetAlphabet(alphabetName), expectedSeq); // Validate Codons lookup method. AminoAcid aminoAcid = Codons.Lookup(seq, Convert.ToInt32(expectedOffset, null)); // Validate amino acids for a given sequence. Assert.AreEqual(aminoAcid.Name.ToString(), expectedAminoAcid); ApplicationLog.WriteLine(string.Format(null, "Translation P2: Amino Acid {0} is expected.", aminoAcid)); ApplicationLog.WriteLine( "Translation P2: Amino Acid validation for a given sequence was completed successfully."); }
public void ValidateVectorViewColViewRemove() { DenseMatrix <string, string, double> denseMatObj = GetDenseMatrix(); IDictionary <string, double> colView = denseMatObj.ColView(0); colView.Remove("R0"); try { double val = colView["R0"]; Assert.IsNotNull(val); Assert.Fail(); } catch (KeyNotFoundException) { Console.WriteLine( "VectorView BVT : Validation of Remove() method successful"); ApplicationLog.WriteLine( "VectorView BVT : Validation of Remove() method successful"); } }
public void ValidateDensePairAnsiColKeysInFile() { DenseMatrix <string, string, double> denseMatObj = GetDenseMatrix(); ParallelOptions parOptObj = new ParallelOptions(); denseMatObj.WriteDenseAnsi(Constants.FastQTempTxtFileName, parOptObj); string[] colkey = DensePairAnsi.ColKeysInFile(Constants.FastQTempTxtFileName); for (int i = 0; i < colkey.Length; i++) { Assert.AreEqual(denseMatObj.ColKeys[i], colkey[i]); } if (File.Exists(Constants.FastQTempTxtFileName)) { File.Delete(Constants.FastQTempTxtFileName); } ApplicationLog.WriteLine( "DensePairAnsi BVT : Validation of ColKeysInFile() method successful"); }
public void InvalidateSetAlphabet() { // Create BAM Parser object using (BAMParser bamParserObj = new BAMParser()) { // TO cover code coverage. try { bamParserObj.Alphabet = Alphabets.DNA; Assert.Fail(); } catch (NotSupportedException ex) { string exceptionMessage = ex.Message; ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "BAM Parser P2 : Validated Exception {0} successfully", exceptionMessage)); Console.WriteLine(string.Format((IFormatProvider)null, "BAM Parser P2 : Validated Exception {0} successfully", exceptionMessage)); } } }
public void ValidateSeqFormatterProperties() { // Gets the expected sequence from the Xml string samFormatterName = _utilityObj._xmlUtil.GetTextValue(Constants.SamFileParserNode, Constants.ParserNameNode); string bamFormatterName = _utilityObj._xmlUtil.GetTextValue(Constants.BamFileParserNode, Constants.ParserNameNode); // Get SequenceAlignmentFormatter class properties. SAMFormatter actualSamFormatter = SequenceAlignmentFormatters.SAM; IList <ISequenceAlignmentFormatter> allFormatters = SequenceAlignmentFormatters.All; BAMFormatter actualBamFormatterName = SequenceAlignmentFormatters.BAM; // Validate Sequence Formatter Assert.AreEqual(samFormatterName, actualSamFormatter.Name); Assert.AreEqual(2, allFormatters.Count); Assert.AreEqual(bamFormatterName, actualBamFormatterName.Name); Console.WriteLine(string.Format((IFormatProvider)null, "SequenceAlignmentFormatter : Type of the parser is validated successfully")); ApplicationLog.WriteLine("Type of the parser is validated successfully"); }
public void ValidateLookupWithOffsetValueSix() { string alphabetName = _utilityObj._xmlUtil.GetTextValue( Constants.SimpleRnaAlphabetNode, Constants.AlphabetNameNode); string expectedSeq = _utilityObj._xmlUtil.GetTextValue( Constants.CodonsNode, Constants.ExpectedNormalString); string expectedAminoAcid = _utilityObj._xmlUtil.GetTextValue( Constants.CodonsNode, Constants.OffsetZeroSixCharsAminoAcid); string expectedOffset = _utilityObj._xmlUtil.GetTextValue( Constants.CodonsNode, Constants.OffsetVaule2); ISequence seq = new Sequence(Utility.GetAlphabet(alphabetName), expectedSeq); // Validate Codons lookup method. AminoAcid aminoAcid = Codons.Lookup(seq, Convert.ToInt32(expectedOffset, null)); // Validate amino acids for a given sequence. Assert.AreEqual(aminoAcid.Name.ToString((IFormatProvider)null), expectedAminoAcid); ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "Translation P1: Amino Acid {0} is expected.", aminoAcid)); ApplicationLog.WriteLine( "Translation P1: Amino Acid validation for a given sequence was completed successfully."); }
public void ValidateAminoAcid() { // Get Node values from XML. string expectedNucleo = Utility._xmlUtil.GetTextValue( Constants.CodonsNode, Constants.Nucleotide); string expectedAminoAcid = Utility._xmlUtil.GetTextValue( Constants.CodonsNode, Constants.AminoAcid); // Create Nucleotide objects. Nucleotide firstNucleo1 = new Nucleotide(expectedNucleo[0], "Uracil"); Nucleotide firstNucleo2 = new Nucleotide(expectedNucleo[1], "Uracil"); Nucleotide firstNucleo3 = new Nucleotide(expectedNucleo[2], "Uracil"); // Validate Codons lookup method. AminoAcid aminoAcid = Codons.Lookup(firstNucleo1, firstNucleo2, firstNucleo3); // Validate amino acids for each triplet. Assert.AreEqual(aminoAcid.Name.ToString(), expectedAminoAcid); ApplicationLog.WriteLine(string.Format(null, "Translation BVT: Amino Acid {0} is expected.", aminoAcid)); ApplicationLog.WriteLine( "Translation BVT: Amino Acid validation for a given triplets of nucleotide was completed successfully."); }
public void InvalidateSAMParseHeaderMBFReader() { string filePath = utilityObj.xmlUtil.GetTextValue( Constants.InvalidSamMBFReaderNode, Constants.FilePathNode); try { using (TextReader reader = new StreamReader(filePath)) { SAMParser.ParseSAMHeader(reader); } Assert.Fail(); } catch (FormatException) { ApplicationLog.WriteLine( "SAM Parser P2 : Successfully validated the exception"); Console.WriteLine( "SAM Parser P2 : Successfully validated the exception"); } }
public void ValidateDnaAlphabetAdd() { // Gets the actual sequence and the alphabet from the Xml string alphabetName = _utilityObj._xmlUtil.GetTextValue(Constants.SimpleDnaAlphabetNode, Constants.AlphabetNameNode); string actualSequence = _utilityObj._xmlUtil.GetTextValue(Constants.SimpleDnaAlphabetNode, Constants.ExpectedSingleChar); ISequence seq = new Sequence(Utility.GetAlphabet(alphabetName), actualSequence); DnaAlphabet alp = DnaAlphabet.Instance; try { alp.Add(seq[0]); Assert.Fail(); } catch (Exception) { // Logs to the NUnit GUI window ApplicationLog.WriteLine("Alphabets BVT: Validation of Add() method completed successfully."); Console.WriteLine("Alphabets BVT: Validation of Add() method completed successfully."); } }
/// <summary> /// Creates a sparse sequence and inserts sequence items of alphabet. /// Creates copy of sparse sequence object using clone() method. /// and Validates if copy of sparse sequence is as expected. /// </summary> /// <param name="alphabet">alphabet instance.</param> private void ValidateSparseSequenceCopyTo(IAlphabet alphabet) { SparseSequence sparseSequence = CreateSparseSequence(alphabet, 10); sparseSequence.IsReadOnly = false; // Copy sequence items to empty array ISequenceItem[] sequenceItems = new ISequenceItem[alphabet.Count + 10]; sparseSequence.CopyTo(sequenceItems, 0); // Validate the copied array. int retrieveIndex = 10; foreach (ISequenceItem item in alphabet) { Assert.AreEqual(item, sequenceItems[retrieveIndex]); Assert.AreEqual(item.Symbol, sequenceItems[retrieveIndex].Symbol); retrieveIndex++; } Console.WriteLine("SparseSequenceBVT: Validation of CopyTo() method is completed"); ApplicationLog.WriteLine("SparseSequenceBVT: Validation of CopyTo() method is completed"); }
public void ValidateMoreThanTwelveCharsDnaTranscribe() { // Get Node values from XML. string alphabetName = utilityObj.xmlUtil.GetTextValue( Constants.SimpleDnaAlphabetNode, Constants.AlphabetNameNode); string expectedSeq = utilityObj.xmlUtil.GetTextValue( Constants.ComplementNode, Constants.DnaSequenceWithMoreThanTwelveChars); string expectedTranscribe = utilityObj.xmlUtil.GetTextValue( Constants.TranscribeNode, Constants.DnaTranscribeForMoreThanTwelveCharsV2); ISequence transcribe = null; Sequence seq = new Sequence(Utility.GetAlphabet(alphabetName), expectedSeq); // Transcribe DNA Symbol. transcribe = Transcription.Transcribe(seq); // Validate transcribe.for a given sequence. Assert.AreEqual(new string(transcribe.Select(a => (char)a).ToArray()), expectedTranscribe); ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "Translation P1: Transcribe {0} is expected.", transcribe)); ApplicationLog.WriteLine( "Translation P1: Transcribe of Single DNA Symbol was validate successfully."); }
public void ValidateVirtualBAMAlignedSequenceListCopyTo() { VirtualAlignedSequenceList <SAMAlignedSequence> virtualASeqList = GetBAMAlignedSequence(Constants.BAMFileWithMultipleAlignedSeqsNode); SAMAlignedSequence[] samAlignedSeqList = new SAMAlignedSequence[virtualASeqList.Count]; // Copy virtual aligned sequence to sam aligned sequence lilst array. virtualASeqList.CopyTo(samAlignedSeqList, 0); // Validate copied aligned sequences. for (int i = 0; i < virtualASeqList.Count; i++) { Assert.AreEqual(samAlignedSeqList[i].QuerySequence.ToString(), virtualASeqList[i].QuerySequence.ToString()); } ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "Virtual AlignedSequenceList Bvt : Validated the VAS CopyTo")); Console.WriteLine(string.Format((IFormatProvider)null, "Virtual AlignedSequenceList Bvt : Validated the VAS CopyTo")); }
/// <summary> /// Passes a valid DNA sequence and validates corresponding transcribe sequence i.e. RNA Sequence /// </summary> /// <param name="sequenceNode">Sequence xml node.</param> /// <param name="revTranscribeNode">Expected transcribe sequence.</param> void ValidateDnaToRnaTranscribe(string sequenceNode, string transcribeNode) { // Get Node values from XML. string alphabetName = utilityObj.xmlUtil.GetTextValue(Constants.SimpleDnaAlphabetNode, Constants.AlphabetNameNode); string expectedSeq = utilityObj.xmlUtil.GetTextValue(Constants.TranscribeNode, sequenceNode); string expectedTranscribe = utilityObj.xmlUtil.GetTextValue(Constants.TranscribeNode, transcribeNode); ISequence transcribe = null; Sequence seq = new Sequence(Utility.GetAlphabet(alphabetName), expectedSeq); // Transcribe DNA Sequence. transcribe = Transcription.Transcribe(seq); // Validate Dna to Rna transcribe. Assert.AreEqual(expectedTranscribe, new string(transcribe.Select(a => (char)a).ToArray())); ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "Translation P1: Transcribe {0} is expected.", transcribe)); ApplicationLog.WriteLine( "Translation P1: Transcribe to Dna to Rna sequence completed successfully."); }
public void ValidateDnaReverseComplementationWithTweleveChars() { // Get Node values from XML. string alphabetName = utilityObj.xmlUtil.GetTextValue( Constants.SimpleDnaAlphabetNode, Constants.AlphabetNameNode); string expectedSeq = utilityObj.xmlUtil.GetTextValue( Constants.ComplementNode, Constants.DnaSequence); string expectedRevComplement = utilityObj.xmlUtil.GetTextValue( Constants.ComplementNode, Constants.DnaRevComplement); ISequence revComplement = null; Sequence seq = new Sequence(Utility.GetAlphabet(alphabetName), expectedSeq); // Reverse Complement DNA Sequence. revComplement = seq.GetReverseComplementedSequence(); // Validate Reverse Complement for a given sequence. Assert.AreEqual(new string(revComplement.Select(a => (char)a).ToArray()), expectedRevComplement); ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "Translation P1: Reverse Complement {0} is expected.", revComplement)); ApplicationLog.WriteLine( "Translation P1: Reverse Complement of twelve DNA characters sequence validated successfully."); }
public void ValidatePaddedDoubleGetInstanceFromSparseEnum() { RowKeyColKeyValue <string, string, double> rowKeyObj = new RowKeyColKeyValue <string, string, double>("R0", "C0", 2); List <RowKeyColKeyValue <string, string, double> > enumObj = new List <RowKeyColKeyValue <string, string, double> >(); enumObj.Add(rowKeyObj); PaddedDouble pdObj = PaddedDouble.GetInstanceFromSparse(enumObj); Assert.AreEqual(1, pdObj.ColCount); Assert.AreEqual(1, pdObj.RowCount); Assert.AreEqual("R0", pdObj.RowKeys[0]); Assert.AreEqual("C0", pdObj.ColKeys[0]); Console.WriteLine( "PaddedDouble BVT : Validation of GetInstanceFromSparse(enum) method successful"); ApplicationLog.WriteLine( "PaddedDouble BVT : Validation of GetInstanceFromSparse(enum) method successful"); }