public void TestSequenceCTor()
{
byte[] b = new byte[6];
b[0] = (byte)'C';
b[1] = (byte)'A';
b[2] = (byte)'A';
b[3] = (byte)'G';
b[4] = (byte)'C';
b[5] = (byte)'T';
string expectedSequence = "CAAGCT";
ISequence sequence = new Sequence(Alphabets.DNA, b);
string actual = "";
foreach (byte bt in sequence)
{
actual += (char)bt;
}
Assert.AreEqual(expectedSequence, actual);
Assert.AreEqual(sequence.Alphabet,Alphabets.DNA);
Assert.AreEqual(sequence.Count, 6);
//
// Test for indexer
Assert.AreEqual(sequence[0], (byte)'C');
Assert.AreEqual(sequence[1], (byte)'A');
Assert.AreEqual(sequence[2], (byte)'A');
Assert.AreEqual(sequence[3], (byte)'G');
Assert.AreEqual(sequence[4], (byte)'C');
Assert.AreEqual(sequence[5], (byte)'T');
}
private void saveButton_Click(object sender, RoutedEventArgs e)
{
if (sequenceTextBox.Text != null)
{
InitializeSaveSequenceFileDialog();
if (saveSequenceFileDialog.ShowDialog() == true)
{
try
{
Fragment toSave = new Fragment();
toSave.Name = sequenceName;
ISequence seq = new Bio.Sequence(Alphabets.DNA, sequence);
toSave.Sequence = seq;
toSave.Length = sequence.Length;
ISequenceFormatter formatter = SequenceFormatters.FindFormatterByFileName(saveSequenceFileDialog.FileName);
formatter.Write(seq);
formatter.Close();
//toSave.Construct.SaveAsBio(saveSequenceFileDialog.FileName);
}
catch (Exception ex)
{
MessageBoxResult result = ModernDialog.ShowMessage(ex.Message, "Exception", MessageBoxButton.OK);
}
}
}
}
public void TestSparseSequenceEnumerator()
{
int i = 0;
ISequence seq = new Sequence(Alphabets.DNA, "ATGC");
var sparseSeq = new SparseSequence(Alphabets.DNA, 0, seq);
foreach (byte item in sparseSeq)
{
Assert.AreEqual(sparseSeq[i++], item);
}
}
public void SimpleFindOneOutputPatternTest()
{
ISequence sequence = new Sequence(DnaAlphabet.Instance, "AGCT");
IPatternFinder patternFinder = new BoyerMoore();
IList<int> actual = patternFinder.FindMatch(sequence, "AGCT");
HashSet<int> expected = new HashSet<int>();
expected.Add(0);
Assert.IsTrue(Compare(expected, actual));
}
public void TestTranscriptionAmbiguousData()
{
ISequence seq = new Sequence(Alphabets.AmbiguousDNA, "MSRWY");
ISequence transcript = Transcription.Transcribe(seq);
Assert.IsTrue(CompareSequenceToString("MSRWY", transcript));
Assert.AreEqual(Alphabets.AmbiguousRNA, transcript.Alphabet);
ISequence reverseTranscript = Transcription.ReverseTranscribe(transcript);
Assert.IsTrue(CompareSequenceToString("MSRWY", reverseTranscript));
Assert.AreEqual(Alphabets.AmbiguousDNA, reverseTranscript.Alphabet);
}
public void TestTranscription()
{
ISequence seq = new Sequence(Alphabets.DNA, "ATGGCG");
ISequence transcript = Transcription.Transcribe(seq);
Assert.IsTrue(CompareSequenceToString("AUGGCG", transcript));
Assert.AreEqual(Alphabets.RNA, transcript.Alphabet);
ISequence reverseTranscript = Transcription.ReverseTranscribe(transcript);
Assert.IsTrue(CompareSequenceToString("ATGGCG", reverseTranscript));
Assert.AreEqual(Alphabets.DNA, reverseTranscript.Alphabet);
}
public void TestTranscriptionSmallCase()
{
ISequence seq = new Sequence(Alphabets.DNA, "atggcg");
ISequence transcript = Transcription.Transcribe(seq);
Assert.IsTrue(CompareSequenceToString("auggcg", transcript));
Assert.AreEqual(Alphabets.RNA, transcript.Alphabet);
ISequence reverseTranscript = Transcription.ReverseTranscribe(transcript);
Assert.IsTrue(CompareSequenceToString("atggcg", reverseTranscript));
Assert.AreEqual(Alphabets.DNA, reverseTranscript.Alphabet);
}
public void PairwiseOverlapProteinSeqAffineGap()
{
string sequenceString1 = "HEAGAWGHEE";
string sequenceString2 = "PAWHEAE";
Sequence sequence1 = new Sequence(Alphabets.Protein, sequenceString1);
Sequence sequence2 = new Sequence(Alphabets.Protein, sequenceString2);
SimilarityMatrix sm = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Blosum50);
int gapPenalty = -8;
PairwiseOverlapAligner overlap = new PairwiseOverlapAligner();
overlap.SimilarityMatrix = sm;
overlap.GapOpenCost = gapPenalty;
overlap.GapExtensionCost = -1;
IList<IPairwiseSequenceAlignment> result = overlap.Align(sequence1, sequence2);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"{0}, Affine; Matrix {1}; GapOpenCost {2}; GapExtenstionCost {3}",
overlap.Name, overlap.SimilarityMatrix.Name, overlap.GapOpenCost, overlap.GapExtensionCost));
foreach (IPairwiseSequenceAlignment sequenceResult in result)
{
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"score {0}", sequenceResult.PairwiseAlignedSequences[0].Score));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"input 0 {0}", sequenceResult.FirstSequence.ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"input 1 {0}", sequenceResult.SecondSequence.ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"result 0 {0}", sequenceResult.PairwiseAlignedSequences[0].FirstSequence.ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"result 1 {0}", sequenceResult.PairwiseAlignedSequences[0].SecondSequence.ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"consesus {0}", sequenceResult.PairwiseAlignedSequences[0].Consensus.ToString()));
}
IList<IPairwiseSequenceAlignment> expectedOutput = new List<IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment align = new PairwiseSequenceAlignment();
PairwiseAlignedSequence alignedSeq = new PairwiseAlignedSequence();
alignedSeq.FirstSequence = new Sequence(Alphabets.Protein, "GAWGHEE");
alignedSeq.SecondSequence = new Sequence(Alphabets.Protein, "PAW-HEA");
alignedSeq.Consensus = new Sequence(Alphabets.AmbiguousProtein, "XAWGHEX");
alignedSeq.Score = 25;
alignedSeq.FirstOffset = 0;
alignedSeq.SecondOffset = 3;
align.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(align);
Assert.IsTrue(CompareAlignment(result, expectedOutput));
}
/// <summary>
/// The extract chains.
/// </summary>
/// <param name="subsequences">
/// The subsequences.
/// </param>
/// <param name="chainId">
/// The sequence id.
/// </param>
/// <returns>
/// The <see cref="List{Chain}"/>.
/// </returns>
public Chain[] ExtractChains(Subsequence[] subsequences, long chainId)
{
var parentChain = commonSequenceRepository.ToLibiadaBaseChain(chainId).ToString();
var sourceSequence = new Sequence(Alphabets.DNA, parentChain);
var result = new Chain[subsequences.Length];
for (int i = 0; i < subsequences.Length; i++)
{
result[i] = subsequences[i].Position.Count == 0
? ExtractSimpleSubsequence(sourceSequence, subsequences[i])
: ExtractJoinedSubsequence(sourceSequence, subsequences[i]);
}
return result;
}
public void TestPcaStep3DeletionInReference()
{
Sequence r = new Sequence(DnaAlphabet.Instance, "CTACGATCGGGG");
// CTACGTGC // TGCGCA is deleted from reference
// GCATCG
// GGGG
Sequence q = new Sequence(DnaAlphabet.Instance, "CTACGTGC");
Sequence q2 = new Sequence(DnaAlphabet.Instance, "GCATCG");
Sequence q3 = new Sequence(DnaAlphabet.Instance, "GGGG");
ComparativeGenomeAssembler asm = new ComparativeGenomeAssembler() { LengthOfMum = 3 };
var output = asm.Assemble(new List<ISequence> { r }, new List<ISequence> { q, q2, q3 });
string res = new string(output.ElementAt(0).Select(a => (char)a).ToArray());
Assert.AreEqual("CTACGTGCATCGGGG", res);
}
/// <summary>
/// This method takes in a MBF sequence and converts it to BioPatML sequence.
/// </summary>
/// <param name="mbfseq">The MBF sequence one is interested in.</param>
/// <returns>Returns the converted BioPatML sequence.</returns>
public QUT.Bio.BioPatML.Sequences.Sequence ParseMBFSequence
(Sequence mbfseq)
{
GenBankMetadata metaData;
#region If sequence is complex type e.g. Genbank file with features
if (mbfseq.Metadata.ContainsKey(Helper.GenBankMetadataKey))
{
//Retrieves our meta data out
metaData = (GenBankMetadata)mbfseq.Metadata[Helper.GenBankMetadataKey];
//Create our BioPatML sequence
QUT.Bio.BioPatML.Sequences.Sequence bioSequence = new QUT.Bio.BioPatML.Sequences.Sequence
(ParseAlphabet(mbfseq), mbfseq.ToString(),
IsCircularStrand(metaData.Locus));
#region Top the BioPatML Sequence with Feature data and sequence name
//Add features to sequence
bioSequence.AddFeatures(ExtractFeatures(metaData));
//Add mbf sequence name to BioPatML sequence
//Create annotation to put in our sequence data like name
AnnotationList jacobiMeta = new AnnotationList();
jacobiMeta.Add("SequenceName", metaData.Locus.Name);
bioSequence.AddAnnotations(jacobiMeta);
#endregion
return bioSequence;
}
#endregion
#region Else we assume it is a simple type e.g. Fasta files
else
{
QUT.Bio.BioPatML.Sequences.Sequence bioSequence = new QUT.Bio.BioPatML.Sequences.Sequence
(ParseAlphabet(mbfseq), mbfseq.ToString(),
false);
AnnotationList jacobiMeta = new AnnotationList();
jacobiMeta.Add("SequenceName", mbfseq.DisplayID);
bioSequence.AddAnnotations(jacobiMeta);
return bioSequence;
}
#endregion
}
public void MultipleFindOneOutputPatternTest()
{
ISequence sequence = new Sequence(DnaAlphabet.Instance, "AGCTAGGTTGGCC");
IList<string> patterns = new List<string>();
patterns.Add("AGCT");
patterns.Add("AAAAA");
IPatternFinder patternFinder = new BoyerMoore();
IDictionary<string, IList<int>> actual = patternFinder.FindMatch(sequence, patterns);
IDictionary<string, HashSet<int>> expected = new Dictionary<string, HashSet<int>>();
HashSet<int> indices = new HashSet<int>();
indices.Add(0);
expected.Add("AGCT", indices);
indices = new HashSet<int>();
expected.Add("AAAAA", indices);
Assert.IsTrue(Compare(expected, actual));
}
public void TestTranscriptionInvalidData()
{
try
{
ISequence seq = new Sequence(Alphabets.AmbiguousRNA, "MSRWY");
ISequence transcript = Transcription.Transcribe(seq);
Assert.Fail();
}
catch (InvalidOperationException)
{
}
try
{
ISequence seq = new Sequence(Alphabets.RNA, "AUGGCG");
ISequence transcript = Transcription.Transcribe(seq);
Assert.Fail();
}
catch (InvalidOperationException)
{
}
try
{
ISequence seq = new Sequence(Alphabets.DNA, "ATGGCG");
ISequence transcript = Transcription.ReverseTranscribe(seq);
Assert.Fail();
}
catch (InvalidOperationException)
{
}
try
{
ISequence seq = new Sequence(Alphabets.AmbiguousDNA, "MSRWY");
ISequence transcript = Transcription.ReverseTranscribe(seq);
Assert.Fail();
}
catch (InvalidOperationException)
{
}
}
public CCSDataSet(Sequence ccs, List<Sequence> subreads, BWAPairwiseAlignment aln)
{
// Call Variants
var results = VariantCaller.LeftAlignIndelsAndCallVariants (aln);
Variants = results.Item2;
Variants.ForEach (p => {
p.StartPosition += aln.AlignedSAMSequence.Pos;
p.RefName = aln.Reference;
});
// Get the ungapped reference
var ccs_aligned = results.Item1.SecondSequence;
// Generate an ungapped reference
var refseq = results.Item1.PairwiseAlignedSequences.First().FirstSequence;
var reference = new Sequence (DnaAlphabet.Instance,
refseq.Where (bp => bp != '-').ToArray (),
false)
{ ID = aln.Reference + "/" + aln.AlignedSAMSequence.Pos + "-" + aln.AlignedSAMSequence.RefEndPos };
var reference_rc = reference.GetReverseComplementedSequence () as Sequence;
Reads = subreads.Select(z => new AlignedSequence(z, reference, reference_rc)).Where( x => (Math.Abs((x.Sequence.Length - reference.Count)) / (double) reference.Count) < 0.2).ToList();
Reads.Insert (0, new AlignedSequence (reference, reference, reference_rc));
ccs.ID = "CCS";
Reads.Insert(1, new AlignedSequence(ccs, reference, reference_rc));
// Now to rejigger the alignments
int[] metaOffSets = Enumerable.Range(0, (int)reference.Count).
Select (i => Reads.Max( r => r.GetInsertsBeforePosition(i))).
ToArray();
Reads.ForEach(r => {
r.ReJiggerAlignment(metaOffSets);
Console.WriteLine(r.Sequence);});
CCS = ccs;
Reference = reference;
Aln = aln;
}
public void TestPcaStep2WithTwoReads()
{
ComparativeGenomeAssembler asm = new ComparativeGenomeAssembler() { LengthOfMum = 9, KmerLength = 9 };
Sequence q = new Sequence(DnaAlphabet.Instance, "AACCTTGGCC");
q.ID = ">read.F:TestPcaStep2WithTwoReads";
Sequence p = new Sequence(DnaAlphabet.Instance, "GGGGGGGGGG");
p.ID = ">read.R:TestPcaStep2WithTwoReads";
CloneLibrary.Instance.AddLibrary("TestPcaStep2WithTwoReads", (float)61, (float)1);
TestPcaAssemble(asm,
new List<Sequence>{
new Sequence(DnaAlphabet.Instance, "AACCTTGGCCCCCACGATCGCGCTAGATCGCATCGATCCCCAACCTTGGCCGGGGGGGGGG", false)
},
new List<ISequence> { q,p },
new List<string> {
"AACCTTGGCC",
"GGGGGGGGGG"
});
}
private void save_Click(object sender, RoutedEventArgs e)
{
if (changeTextBox.Text != null)
{
InitializeSaveSequenceFileDialog();
if (saveEditSequenceFileDialog.ShowDialog() == true)
{
try
{
string sequenceToSave = changeTextBox.Text;
ISequence seq = new Bio.Sequence(Alphabets.DNA, sequenceToSave);
ISequenceFormatter formatter = SequenceFormatters.FindFormatterByFileName(saveEditSequenceFileDialog.FileName);
formatter.Write(seq);
formatter.Close();
}
catch (Exception ex)
{
MessageBoxResult result = ModernDialog.ShowMessage(ex.Message, "Exception", MessageBoxButton.OK);
}
}
}
}
public static void Test1BPDeletionCall()
{
string seq1seq = "ATACCCCTT";
string seq2seq = "ATA-CCCTT".Replace("-", String.Empty);
int[] seq2qual = new int[] { 30, 30, 30, 2, 30, 30, 30, 30 };
var refseq = new Sequence(AmbiguousDnaAlphabet.Instance, seq1seq, false);
var query = new Sequence (AmbiguousDnaAlphabet.Instance, seq2seq, false);
NeedlemanWunschAligner aligner = new NeedlemanWunschAligner ();
var aln = aligner.Align (refseq, query).First();
// Need to add in the QV Values.
ConvertAlignedSequenceToQualSeq(aln, seq2qual);
var variants = VariantCaller.CallVariants (aln);
Assert.AreEqual (variants.Count, 1);
var variant = variants.First ();
Assert.AreEqual (2, variant.QV);
Assert.AreEqual (2, variant.StartPosition);
Assert.AreEqual (VariantType.INDEL, variant.Type);
var vi = variant as IndelVariant;
Assert.AreEqual ("C", vi.InsertedOrDeletedBases);
Assert.AreEqual ('C', vi.HomopolymerBase);
Assert.AreEqual (4, vi.HomopolymerLengthInReference);
Assert.AreEqual (true, vi.InHomopolymer);
Assert.AreEqual (vi.InsertionOrDeletion, IndelType.Deletion);
}
public AlignedSequence(Sequence read, Sequence reference, Sequence reference_rc)
{
// Align the read and reference
var algo = new NeedlemanWunschAligner ();
algo.GapOpenCost = -20;
algo.GapExtensionCost = -19;
algo.SimilarityMatrix = new DiagonalSimilarityMatrix (20, -20);
var aln = algo.Align (read, reference).First ().AlignedSequences.First () as PairwiseAlignedSequence;
var reverse_aln = algo.Align (read, reference_rc).First ().AlignedSequences.First () as PairwiseAlignedSequence;
Sequence Ref, Query;
Name = read.ID;
if (aln.Score < reverse_aln.Score) {
aln = reverse_aln;
Query = (aln.Sequences [0] as Sequence).GetReverseComplementedSequence () as Sequence;
Ref = (aln.Sequences [1] as Sequence).GetReverseComplementedSequence () as Sequence;
Name = Name + "_RC";
} else {
Query = (aln.Sequences [0] as Sequence);
Ref = (aln.Sequences [1] as Sequence);
}
// Now calculate the offsets
OffSets = new int[reference.Count];
int refBases = -1;
for (int i = 0; i < Ref.Count; i++) {
if (Ref [i] != '-') {
refBases++;
OffSets [refBases] = i;
}
}
Sequence = Query.ConvertToString ();
//Console.WriteLine (read.ID);
//Console.WriteLine ((aln.Sequences [0] as Sequence).ConvertToString ());
//Console.WriteLine ((aln.Sequences [1] as Sequence).ConvertToString ());
}
public void ValidateBioHPCCtor()
{
// Gets the search query parameter and their values.
string alphabetName = utilityObj.xmlUtil.GetTextValue(Constants.BioHPCAsynchronousResultsNode, Constants.AlphabetNameNode);
string querySequence = utilityObj.xmlUtil.GetTextValue(Constants.BioHPCAsynchronousResultsNode, Constants.QuerySequency);
string queryDatabaseValue = utilityObj.xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode,
Constants.DatabaseValue);
string email = utilityObj.xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode,
Constants.EmailAdress);
string queryProgramValue = utilityObj.xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode,
Constants.ProgramValue);
string queryDatabaseParameter = utilityObj.xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode,
Constants.DatabaseParameter);
string queryProgramParameter = utilityObj.xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode,
Constants.ProgramParameter);
string expect = utilityObj.xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode, Constants.Expectparameter);
string emailNotify = utilityObj.xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode, Constants.EmailNotifyParameterNode);
string jobName = utilityObj.xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode, Constants.JobNameParameterNode);
string expectValue = utilityObj.xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode, Constants.ExpectNode);
string emailNotifyValue = utilityObj.xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode, Constants.EmailNotifyNode);
string jobNameValue = utilityObj.xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode, Constants.JobNameNode);
Sequence seq = new Sequence(Utility.GetAlphabet(alphabetName),
querySequence);
// create BioHPC Blast Web Service object.
IBlastServiceHandler service = new BioHPCBlastHandler();
ConfigParameters configParams = new ConfigParameters();
configParams.EmailAddress = email;
configParams.Password = string.Empty;
//configParams.UseBrowserProxy = true;
service.Configuration = configParams;
BlastParameters searchParams = new BlastParameters();
// Set Request parameters.
searchParams.Add(queryDatabaseParameter, queryDatabaseValue);
searchParams.Add(queryProgramParameter, queryProgramValue);
searchParams.Add(expect, expectValue);
searchParams.Add(emailNotify, emailNotifyValue);
searchParams.Add(jobName, jobNameValue);
try
{
// Create a request without passing sequence.
string reqId = service.SubmitRequest(seq, searchParams);
Assert.IsNotNull(reqId);
}
catch (WebException ex)
{
Assert.Fail();
Console.WriteLine(string.Format((IFormatProvider)null,
"BioHPC Blast Bvt : Connection not successful with error '{0}'",
ex.Message));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"BioHPC Blast Bvt : Connection not successful with error '{0}'",
ex.Message));
}
finally
{
if (service != null)
((IDisposable)service).Dispose();
}
}
/// <summary>
/// Validate Cancel submitted job by passing job id.
/// <param name="nodeName">different alphabet node name</param>
/// </summary>
void ValidateCancelSubmittedJob(
string nodeName,
RequestType type)
{
// Gets the search query parameter and their values.
string alphabetName = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string querySequence = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QuerySequency);
string queryDatabaseValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DatabaseValue);
string email = Constants.EmailForWS; ;
string queryProgramValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ProgramValue);
string queryDatabaseParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DatabaseParameter);
string queryProgramParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ProgramParameter);
string expect = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Expectparameter);
string emailNotify = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EmailNotifyParameterNode);
string jobName = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.JobNameParameterNode);
string expectValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExpectNode);
string emailNotifyValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EmailNotifyNode);
string jobNameValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.JobNameNode);
// Set Blast Parameters
Sequence seq = new Sequence(Utility.GetAlphabet(alphabetName),
querySequence);
IBlastServiceHandler service = new BioHPCBlastHandler();
ConfigParameters configParameters = new ConfigParameters();
configParameters.EmailAddress = email;
configParameters.Password = String.Empty;
configParameters.UseBrowserProxy = true;
service.Configuration = configParameters;
BlastParameters searchParams = new BlastParameters();
// Set Request parameters.
searchParams.Add(queryDatabaseParameter, queryDatabaseValue);
searchParams.Add(queryProgramParameter, queryProgramValue);
searchParams.Add(expect, expectValue);
searchParams.Add(emailNotify, emailNotifyValue);
searchParams.Add(jobName, jobNameValue);
string reqId = String.Empty;
// Waiting for the any previous request to get completed.
Thread.Sleep(150000);
// Create a request without passing sequence.
switch (type)
{
case RequestType.StrSubmit:
reqId = service.SubmitRequest(seq, searchParams);
break;
case RequestType.LstSubmit:
IList<ISequence> lstSeq = new List<ISequence>();
lstSeq.Add(seq);
reqId = service.SubmitRequest(lstSeq, searchParams);
break;
}
// Cancel subitted job.
bool result = service.CancelRequest(reqId);
// validate the cancelled job.
Assert.IsTrue(result);
Console.WriteLine(string.Concat(
"BioHPC Blast Bvt : Submitted job cancelled was successfully. ",
queryProgramValue));
}
/// <summary>
/// Validate general http request status by
/// differnt parameters for BioHPC Blast Web Service.
/// <param name="nodeName">different alphabet node name</param>
/// </summary>
void ValidateBioHPCGeneralGetRequestStatusMethod(string nodeName,
string moleculeType)
{
// Gets the search query parameter and their values.
string alphabetName = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string querySequence = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QuerySequency);
string queryDatabaseValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DatabaseValue);
string queryProgramValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ProgramValue);
string queryDatabaseParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DatabaseParameter);
string queryProgramParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ProgramParameter);
string email = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EmailAdress);
string expect = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Expectparameter);
string emailNotify = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EmailNotifyParameterNode);
string jobName = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.JobNameParameterNode);
string expectValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExpectNode);
string emailNotifyValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EmailNotifyNode);
string jobNameValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.JobNameNode);
// Create a sequence.
Sequence seq = new Sequence(Utility.GetAlphabet(alphabetName),
querySequence);
// Set Service confiruration parameters true.
IBlastServiceHandler service = new BioHPCBlastHandler();
ConfigParameters configParameters = new ConfigParameters();
configParameters.EmailAddress = email;
configParameters.Password = String.Empty;
configParameters.UseBrowserProxy = true;
service.Configuration = configParameters;
// Create search parameters object.
BlastParameters queryParams = new BlastParameters();
// Add mandatory parameter values to search query parameters.
queryParams.Add(queryDatabaseParameter, queryDatabaseValue);
queryParams.Add(queryProgramParameter, queryProgramValue);
queryParams.Add(expect, expectValue);
queryParams.Add(emailNotify, emailNotifyValue);
queryParams.Add(jobName, jobNameValue);
// Create a request
// Waiting for the any previous request to get completed.
Thread.Sleep(150000);
string reqId = service.SubmitRequest(seq, queryParams);
// validate request identifier.
Assert.IsNotNull(reqId);
// submit request identifier and get the status
ServiceRequestInformation reqInfo =
service.GetRequestStatus(reqId);
// Validate job status.
if (reqInfo.Status != ServiceRequestStatus.Waiting
&& reqInfo.Status != ServiceRequestStatus.Ready
&& reqInfo.Status != ServiceRequestStatus.Queued)
{
string error = ApplicationLog.WriteLine(string.Concat(
"Unexpected error ", reqInfo.Status));
Assert.Fail(error);
Console.WriteLine(string.Concat(
"Unexpected error ", reqInfo.Status));
}
else
{
Console.WriteLine(string.Concat(
"Request status ", reqInfo.Status));
}
}
/// <summary>
/// Validate general fetching results.by passing
/// differnt parameters for BioHPC Blast web service.
/// <param name="nodeName">xml node name.</param>
/// <param name="isFetchSynchronous">Is Fetch Synchronous?</param>
/// </summary>
void ValidateBioHPCBlastResultsFetch(
string nodeName, bool isFetchSynchronous)
{
// Gets the search query parameter and their values.
string alphabetName = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string querySequence = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QuerySequency);
string queryDatabaseValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DatabaseValue);
string email = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EmailAdress);
string queryProgramValue = utilityObj.xmlUtil.GetTextValue(
nodeName,
Constants.ProgramValue);
string queryDatabaseParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DatabaseParameter);
string queryProgramParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ProgramParameter);
string expectedHitId = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.HitID);
string expectedAccession = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.HitAccession);
string expectedResultCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ResultsCount);
string expectedHitsCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.HitsCount);
string expectedEntropyStatistics =
utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EntropyStatistics);
string expectedKappaStatistics = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.KappaStatistics);
string expectedLambdaStatistics = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LambdaStatistics);
string expectedLength = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Length);
int maxAttempts = int.Parse(utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.MaxAttemptsNode), (IFormatProvider)null);
int waitingTime = int.Parse(utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.WaitTimeNode), (IFormatProvider)null);
string expect = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Expectparameter);
string emailNotify = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EmailNotifyParameterNode);
string jobName = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.JobNameParameterNode);
string expectValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExpectNode);
string emailNotifyValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EmailNotifyNode);
string jobNameValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.JobNameNode);
object responseResults = null;
Sequence seq = new Sequence(
Utility.GetAlphabet(alphabetName),
querySequence);
// create BioHPC Blast Web Service object.
IBlastServiceHandler service = new BioHPCBlastHandler();
ConfigParameters configPams = new ConfigParameters();
configPams.EmailAddress = email;
configPams.Password = String.Empty;
configPams.UseBrowserProxy = true;
service.Configuration = configPams;
BlastParameters searchParams = new BlastParameters();
// Set Request parameters.
searchParams.Add(queryDatabaseParameter, queryDatabaseValue);
searchParams.Add(queryProgramParameter, queryProgramValue);
searchParams.Add(expect, expectValue);
searchParams.Add(emailNotify, emailNotifyValue);
searchParams.Add(jobName, jobNameValue);
// Create a request without passing sequence.
string reqId = service.SubmitRequest(seq, searchParams);
// validate request identifier.
Assert.IsNotNull(reqId);
ServiceRequestInformation info = service.GetRequestStatus(reqId);
if (info.Status != ServiceRequestStatus.Waiting
&& info.Status != ServiceRequestStatus.Ready
&& info.Status != ServiceRequestStatus.Queued)
{
string err =
ApplicationLog.WriteLine("Unexpected status: '{0}'",
info.Status);
Assert.Fail(err);
}
// get async results, poll until ready
int attempt = 1;
while (attempt <= maxAttempts
&& info.Status != ServiceRequestStatus.Error
&& info.Status != ServiceRequestStatus.Ready)
{
++attempt;
if (isFetchSynchronous)
{
info = service.GetRequestStatus(reqId);
Thread.Sleep(
info.Status == ServiceRequestStatus.Waiting
|| info.Status == ServiceRequestStatus.Queued
? waitingTime * attempt : 0);
}
else
{
Thread.Sleep(
info.Status == ServiceRequestStatus.Waiting
|| info.Status == ServiceRequestStatus.Queued ?
waitingTime * attempt : 0);
info = service.GetRequestStatus(reqId);
}
}
IBlastParser blastXmlParser = new BlastXmlParser();
responseResults = blastXmlParser.Parse(
new StringReader(service.GetResult(reqId, searchParams)));
Assert.IsNotNull(responseResults);
List<BlastResult> eBlastResults =
responseResults as List<BlastResult>;
Assert.IsNotNull(eBlastResults);
Assert.AreEqual(eBlastResults.Count.ToString(
(IFormatProvider)null), expectedResultCount);
Assert.AreEqual(eBlastResults[0].Records.Count.ToString((
IFormatProvider)null), expectedResultCount);
BlastSearchRecord record = eBlastResults[0].Records[0];
Assert.AreEqual(record.Statistics.Kappa.ToString(
(IFormatProvider)null), expectedKappaStatistics);
Assert.AreEqual(record.Statistics.Lambda.ToString(
(IFormatProvider)null), expectedLambdaStatistics);
Assert.AreEqual(record.Statistics.Entropy.ToString(
(IFormatProvider)null), expectedEntropyStatistics);
Assert.AreEqual(record.Hits.Count.ToString(
(IFormatProvider)null), expectedHitsCount);
Hit hit = record.Hits[0];
Assert.AreEqual(hit.Accession, expectedAccession);
Assert.AreEqual(hit.Length.ToString((IFormatProvider)null),
expectedLength);
Assert.AreEqual(hit.Id.ToString((IFormatProvider)null),
expectedHitId);
Assert.AreEqual(hit.Hsps.Count.ToString((IFormatProvider)null),
expectedResultCount);
Console.WriteLine(string.Format((IFormatProvider)null,
"BioHPC Blast BVT : Hits count '{0}'.", eBlastResults.Count));
Console.WriteLine(string.Format((IFormatProvider)null,
"BioHPC Blast BVT : Accession '{0}'.", hit.Accession));
Console.WriteLine(string.Format((IFormatProvider)null,
"BioHPC Blast BVT : Hit Id '{0}'.", hit.Id));
Console.WriteLine(string.Format((IFormatProvider)null,
"BioHPC Blast BVT : Hits Count '{0}'.", hit.Hsps.Count));
// Validate the results Synchronously with the results got earlier.
if (isFetchSynchronous)
{
IList<BlastResult> syncBlastResults =
service.FetchResultsSync(reqId, searchParams) as List<BlastResult>;
Assert.IsNotNull(syncBlastResults);
if (null != eBlastResults[0].Records[0].Hits
&& 0 < eBlastResults[0].Records[0].Hits.Count
&& null != eBlastResults[0].Records[0].Hits[0].Hsps
&& 0 < eBlastResults[0].Records[0].Hits[0].Hsps.Count)
{
Assert.AreEqual(
eBlastResults[0].Records[0].Hits[0].Hsps[0].QuerySequence,
syncBlastResults[0].Records[0].Hits[0].Hsps[0].QuerySequence);
}
else
{
ApplicationLog.WriteLine(
"No significant hits found with the these parameters.");
Console.WriteLine(
"No significant hits found with the these parameters.");
}
}
}
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>
/// Return a new sequence representing this sequence with the orientation reversed.
/// </summary>
public ISequence GetReversedSequence()
{
byte[] values = new byte[this.Count];
Helper.Copy(this._sequenceData, values, this._sequenceData.GetLongLength());
Array.Reverse(values);
Sequence seq = new Sequence { _sequenceData = values, Alphabet = this.Alphabet, ID = this.ID, Count = this.Count };
if (this._metadata != null)
seq._metadata = new Dictionary<string, object>(this._metadata);
return seq;
}
/// <summary>
/// Calculation method.
/// </summary>
/// <param name="chains">
/// The chains.
/// </param>
/// <param name="calculators">
/// The calculators.
/// </param>
/// <param name="links">
/// The links.
/// </param>
/// <param name="rotate">
/// The rotate flag.
/// </param>
/// <param name="complementary">
/// The complementary flag.
/// </param>
/// <param name="rotationLength">
/// The rotation length.
/// </param>
/// <returns>
/// The <see cref="T:double[][]"/>.
/// </returns>
public static double[][] Calculate(Chain[][] chains, IFullCalculator[] calculators, Link[] links, bool rotate, bool complementary, uint? rotationLength)
{
var characteristics = new double[chains.Length][];
for (int i = 0; i < chains.Length; i++)
{
characteristics[i] = new double[calculators.Length];
for (int j = 0; j < calculators.Length; j++)
{
if (complementary)
{
var sourceSequence = new Sequence(Alphabets.DNA, chains[i][j].ToString());
var complementarySequence = sourceSequence.GetReverseComplementedSequence();
chains[i][j] = new Chain(complementarySequence.ConvertToString());
}
if (rotate)
{
var building = chains[i][j].Building.Rotate(rotationLength ?? 0);
var newSequence = building.Select(t => new ValueInt(t)).Cast<IBaseObject>().ToList();
chains[i][j] = new Chain(newSequence);
}
chains[i][j].FillIntervalManagers();
characteristics[i][j] = calculators[j].Calculate(chains[i][j], links[j]);
}
}
return characteristics;
}
/// <summary>
/// Return a new sequence representing a range (subsequence) of this sequence.
/// </summary>
/// <param name="start">The index of the first symbol in the range.</param>
/// <param name="length">The number of symbols in the range.</param>
/// <returns>The sub-sequence.</returns>
public ISequence GetSubSequence(long start, long length)
{
if (start >= this.Count)
{
throw new ArgumentOutOfRangeException("start");
}
if (start + length > this.Count)
{
throw new ArgumentOutOfRangeException("length");
}
byte[] subSequence = new byte[length];
for (long index = 0; index < length; index++)
{
subSequence[index] = this._sequenceData[start + index];
}
Sequence seq = new Sequence { _sequenceData = subSequence, Alphabet = this.Alphabet, ID = this.ID, Count = subSequence.Length };
if (this._metadata != null)
seq._metadata = new Dictionary<string, object>(this._metadata);
return seq;
}
/// <summary>
/// Return a new sequence representing the reverse complement of this sequence.
/// </summary>
public ISequence GetReverseComplementedSequence()
{
if (!this.Alphabet.IsComplementSupported)
{
throw new InvalidOperationException(Properties.Resource.ComplementNotFound);
}
byte[] reverseComplemented = new byte[this.Count];
this.Alphabet.TryGetComplementSymbol(this._sequenceData, out reverseComplemented);
Array.Reverse(reverseComplemented);
Sequence seq = new Sequence { _sequenceData = reverseComplemented, Alphabet = this.Alphabet, ID = this.ID, Count = this.Count };
if (this._metadata != null)
seq._metadata = new Dictionary<string, object>(this._metadata);
return seq;
}
/// <summary>
/// Convert given range containing any sequence (other than BED) to Bio.Sequence object
/// </summary>
/// <param name="userSelectedRanges">Range of cells</param>
/// <param name="treatBlankCellsAsGaps">Flag to treat blank cells as gaps</param>
/// <param name="alphabetType">Molecule Type</param>
/// <param name="sequenceId">Sequence Identifier</param>
/// <returns>Sequence object</returns>
public static ISequence RangeToSequence(IList<Range> userSelectedRanges, bool treatBlankCellsAsGaps, string alphabetType, string sequenceId)
{
StringBuilder builder = new StringBuilder();
string cellValue = string.Empty;
foreach (Range range in userSelectedRanges)
{
foreach (Range currentCell in range.Cells)
{
// if cell has value, and its row and column is not hidden
if (currentCell != null && currentCell.Value2 != null && !(currentCell.EntireColumn.Hidden || currentCell.EntireRow.Hidden))
{
cellValue = currentCell.Value2.ToString();
if (string.IsNullOrWhiteSpace(cellValue))
{
if (treatBlankCellsAsGaps)
{
builder.Append(Gap);
}
}
else
{
builder.Append(cellValue);
}
}
else if (treatBlankCellsAsGaps && !(currentCell.EntireColumn.Hidden || currentCell.EntireRow.Hidden))
{
builder.Append(Gap);
}
}
}
string sequenceString = builder.ToString();
IAlphabet alphabet = null;
foreach (IAlphabet alphabetSet in Alphabets.All)
{
if (0 == string.Compare(alphabetSet.Name, alphabetType, true))
{
alphabet = alphabetSet;
break;
}
}
if (null == alphabet)
{
byte[] sequenceBytes = sequenceString.Select(a => (byte)a).ToArray();
alphabet = Alphabets.AutoDetectAlphabet(sequenceBytes, 0, sequenceBytes.Length, null);
}
if (alphabet == null)
{
throw new Exception(Properties.Resources.CannotFindMatchingAlphabet);
}
Sequence sequence = new Sequence(alphabet, sequenceString);
sequence.ID = sequenceId;
return sequence;
}
public void InValidateSubSequenceWithInvalidAccessionID()
{
// Get Values from XML node.
string sequence = utilityObj.xmlUtil.GetTextValue(
Constants.LocationWithDotOperatorNode,
Constants.ExpectedSequence);
string location = utilityObj.xmlUtil.GetTextValue(
Constants.LocationWithDotOperatorNode,
Constants.Location);
string alphabet = utilityObj.xmlUtil.GetTextValue(
Constants.LocationWithDotOperatorNode,
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);
loc.Accession = "Invalid";
// Get sequence using location of the sequence with operator.
try
{
loc.GetSubSequence(seqObj);
Assert.Fail();
}
catch (ArgumentException)
{
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"GenBankFeatures P2 : Validate the exception successfully"));
}
Dictionary<string, ISequence> refSeq = null;
// Validate GetSubSequence method with null location.
try
{
loc.GetSubSequence(null, refSeq);
Assert.Fail();
}
catch (ArgumentNullException)
{
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"GenBankFeatures P2 : Validate the exception successfully"));
}
}
/// <summary>
/// Given two byte arrays representing a pairwise alignment, shift them so
/// that all deletions start as early as possible. For example:
///
/// <code>
/// TTTTAAAATTTT -> Converts to -> TTTTAAAATTTT
/// TTTTAA--TTTT TTTT--AATTTT
/// </code>
///
/// This function takes a IPairwiseSequenceAlignment and assumes that the first sequence is the reference and second
/// sequence is the query. It returns a new Pairwise sequence alignment with all of the indels left aligned as well as a list of variants.
/// </summary>
/// <param name="aln">Aln. The second sequence should be of type QualitativeSequence or Sequence</param>
/// <param name="callVariants">callVariants. If true, it will call variants, otherwise the second half of tuple will be null. </param>
public static Tuple<IPairwiseSequenceAlignment, List<Variant>> LeftAlignIndelsAndCallVariants(IPairwiseSequenceAlignment aln, bool callVariants = true) {
if (aln == null) {
throw new NullReferenceException ("aln");
}
if (aln.PairwiseAlignedSequences == null || aln.PairwiseAlignedSequences.Count != 1) {
throw new ArgumentException ("The pairwise aligned sequence should only have one alignment");
}
var frstAln = aln.PairwiseAlignedSequences.First ();
var seq1 = frstAln.FirstSequence;
var seq2 = frstAln.SecondSequence;
if (seq1 == null) {
throw new NullReferenceException ("seq1");
} else if (seq2 == null) {
throw new NullReferenceException ("seq2");
}
//TODO: Might implement an ambiguity check later.
#if FALSE
if (seq1.Alphabet.HasAmbiguity || seq2.Alphabet.HasAmbiguity) {
throw new ArgumentException ("Cannot left align sequences with ambiguous symbols.");
}
#endif
// Note we have to copy unless we can guarantee the array will not be mutated.
byte[] refseq = seq1.ToArray ();
ISequence newQuery;
List<Variant> variants = null;
// Call variants for a qualitative sequence
if (seq2 is QualitativeSequence) {
var qs = seq2 as QualitativeSequence;
var query = Enumerable.Zip (qs, qs.GetQualityScores (), (bp, qv) => new BPandQV (bp, (byte)qv, false)).ToArray ();
AlignmentUtils.LeftAlignIndels (refseq, query);
AlignmentUtils.VerifyNoGapsOnEnds (refseq, query);
if (callVariants) {
variants = VariantCaller.CallVariants (refseq, query, seq2.IsMarkedAsReverseComplement());
}
var newQueryQS = new QualitativeSequence (qs.Alphabet,
qs.FormatType,
query.Select (z => z.BP).ToArray (),
query.Select (p => p.QV).ToArray (),
false);
newQueryQS.Metadata = seq2.Metadata;
newQuery = newQueryQS;
} else if (seq2 is Sequence) { // For a sequence with no QV values.
var qs = seq2 as Sequence;
var query = qs.Select (v => new BPandQV (v, 0, false)).ToArray();
AlignmentUtils.LeftAlignIndels (refseq, query);
AlignmentUtils.VerifyNoGapsOnEnds (refseq, query);
// ISequence does not have a setable metadata
var newQueryS = new Sequence(qs.Alphabet, query.Select(z=>z.BP).ToArray(), false);
newQueryS.Metadata = seq2.Metadata;
if (callVariants) {
variants = VariantCaller.CallVariants (refseq, query, seq2.IsMarkedAsReverseComplement());
}
newQuery = newQueryS;
} else {
throw new ArgumentException ("Can only left align indels if the query sequence is of type Sequence or QualitativeSequence.");
}
if (aln.FirstSequence != null && aln.FirstSequence.ID != null) {
foreach (var v in variants) {
v.RefName = aln.FirstSequence.ID;
}
}
var newRef = new Sequence (seq1.Alphabet, refseq, false);
newRef.ID = seq1.ID;
newRef.Metadata = seq1.Metadata;
newQuery.ID = seq2.ID;
var newaln = new PairwiseSequenceAlignment (aln.FirstSequence, aln.SecondSequence);
var pas = new PairwiseAlignedSequence ();
pas.FirstSequence = newRef;
pas.SecondSequence = newQuery;
newaln.Add (pas);
return new Tuple<IPairwiseSequenceAlignment, List<Variant>> (newaln, variants);
}
/// <summary>
/// Compute overlap's simple-style melting temperature.
/// </summary>
/// <returns>Overlap's Tm.</returns>
public double GetSimpleMeltingTemperature()
{
double T = 0.0;
Sequence upper = null;
upper = new Sequence(Alphabets.AmbiguousDNA, this.Sequence.ToString().ToUpper());
for (long index = 0; index < upper.Count; index++)
{
T += SimpleT[upper[index]];
}
return T;
}
public void ValidateProcessRequestThread()
{
// Gets the search query parameter and their values.
string alphabetName = utilityObj.xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode, Constants.AlphabetNameNode);
string querySequence = utilityObj.xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode, Constants.QuerySequency);
string queryDatabaseValue = utilityObj.xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode, Constants.DatabaseValue);
string email = Constants.EmailForWS;
string queryProgramValue = utilityObj.xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode, Constants.ProgramValue);
string queryDatabaseParameter = utilityObj.xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode, Constants.DatabaseParameter);
string queryProgramParameter = utilityObj.xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode, Constants.ProgramParameter);
string expect = utilityObj.xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode, Constants.Expectparameter);
string emailNotify = utilityObj.xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode, Constants.EmailNotifyParameterNode);
string jobName = utilityObj.xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode, Constants.JobNameParameterNode);
string expectValue = utilityObj.xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode, Constants.ExpectNode);
string emailNotifyValue = utilityObj.xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode, Constants.EmailNotifyNode);
string jobNameValue = utilityObj.xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode, Constants.JobNameNode);
// Set Blast Parameters
Sequence seq = new Sequence(Utility.GetAlphabet(alphabetName),
querySequence);
BioHPCBlastHandler service = new BioHPCBlastHandler();
try
{
ConfigParameters configParameters = new ConfigParameters();
configParameters.EmailAddress = email;
configParameters.Password = String.Empty;
configParameters.UseBrowserProxy = true;
service.Configuration = configParameters;
service.RequestCompleted += new EventHandler<BlastRequestCompletedEventArgs>(service_RequestCompleted);
BlastParameters searchParams = new BlastParameters();
// Set Request parameters.
searchParams.Add(queryDatabaseParameter, queryDatabaseValue);
searchParams.Add(queryProgramParameter, queryProgramValue);
searchParams.Add(expect, expectValue);
searchParams.Add(emailNotify, emailNotifyValue);
searchParams.Add(jobName, jobNameValue);
string reqId = String.Empty;
// Waiting for the any previous request to get completed.
Thread.Sleep(150000);
// Create a request without passing sequence.
reqId = service.SubmitRequest(seq, searchParams);
// Cancel subitted job.
bool result = service.CancelRequest(reqId);
// validate the cancelled job.
Assert.IsTrue(result);
}
finally
{
if (service != null)
service.Dispose();
}
}