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");
}