/// <summary>
/// Does the logic behind the sequence simulation
/// </summary>
internal void DoSimulation(SimulatorWindow window, string outputFileName, SimulatorSettings settings)
{
FileInfo file = new FileInfo(outputFileName);
if (!file.Directory.Exists)
{
throw new ArgumentException("Could not write to the output directory for " + outputFileName);
}
if (settings.OutputSequenceCount <= 0)
{
throw new ArgumentException("'Max Output Sequences Per File' should be greater than zero.");
}
if (settings.SequenceLength <= 0)
{
throw new ArgumentException("'Mean Output Length' should be greater than zero.");
}
string filePrefix;
if (String.IsNullOrEmpty(file.Extension))
{
filePrefix = file.FullName;
}
else
{
filePrefix = file.FullName.Substring(0, file.FullName.IndexOf(file.Extension));
}
string filePostfix = "_{0}.fa";
int seqCount = (settings.DepthOfCoverage * Sequence.Count) / settings.SequenceLength;
int fileCount = seqCount / settings.OutputSequenceCount;
if (seqCount % settings.OutputSequenceCount != 0)
{
fileCount++;
}
window.UpdateSimulationStats(seqCount, fileCount);
if (results == null)
{
results = new List <ISequence>();
}
else
{
results.Clear();
}
int fileIndex = 1;
FastaFormatter formatter = new FastaFormatter();
for (int i = 0; i < seqCount; i++)
{
results.Add(CreateSubsequence(settings, i));
if (results.Count >= settings.OutputSequenceCount)
{
FileInfo outFile = new FileInfo(filePrefix + string.Format(filePostfix, fileIndex++));
formatter.Format(results, outFile.FullName);
results.Clear();
}
}
if (results.Count > 0)
{
FileInfo outFile = new FileInfo(filePrefix + string.Format(filePostfix, fileIndex++));
formatter.Format(results, outFile.FullName);
}
window.NotifySimulationComplete();
}
public void FastaFormatterWithParseValidateFormat()
{
// Gets the expected sequence from the Xml
string filePath = _utilityObj._xmlUtil.GetTextValue(Constants.SimpleFastaNodeName,
Constants.FilePathNode);
Assert.IsTrue(File.Exists(filePath));
// Logs information to the log file
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"FastA Formatter BVT: File Exists in the Path '{0}'.", filePath));
using (FastaParser parser = new FastaParser())
{
FastaFormatter formatter = new FastaFormatter();
// Read the original file
IList <ISequence> seqsOriginal = null;
seqsOriginal = parser.Parse(filePath);
Assert.IsNotNull(seqsOriginal);
// Use the formatter to write the original sequences to a temp file
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"FastA Formatter BVT: Creating the Temp file '{0}'.",
Constants.FastaTempFileName));
using (TextWriter writer = new StreamWriter(Constants.FastaTempFileName))
{
foreach (Sequence s in seqsOriginal)
{
formatter.Format(s, writer);
}
}
// Read the new file, then compare the sequences
IList <ISequence> seqsNew = null;
seqsNew = parser.Parse(Constants.FastaTempFileName);
Assert.IsNotNull(seqsNew);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"FastA Formatter BVT: New Sequence is '{0}'.",
seqsNew[0].ToString()));
// Now compare the sequences.
int countOriginal = seqsOriginal.Count();
int countNew = seqsNew.Count();
Assert.AreEqual(countOriginal, countNew);
ApplicationLog.WriteLine("The Number of sequences are matching.");
int i;
for (i = 0; i < countOriginal; i++)
{
Assert.AreEqual(seqsOriginal[i].ID, seqsNew[i].ID);
string orgSeq = seqsOriginal[i].ToString();
string newSeq = seqsNew[i].ToString();
Assert.AreEqual(orgSeq, newSeq);
Console.WriteLine(string.Format((IFormatProvider)null,
"FastA Formatter BVT: The FASTA sequences '{0}' are matching with Format() method and is as expected.",
seqsNew[i].ID));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"FastA Formatter BVT: The FASTA sequences '{0}' are matching with Format() method.",
seqsNew[i].ID));
}
}
// Passed all the tests, delete the tmp file. If we failed an Assert,
// the tmp file will still be there in case we need it for debugging.
File.Delete(Constants.FastaTempFileName);
ApplicationLog.WriteLine("Deleted the temp file created.");
}
/// <summary>
/// CreateJob() to get job id and control id and Submit job
/// using input sequence with job id and control id
/// </summary>
/// <param name="sequence">input sequences</param>
/// <param name="parameters">input params</param>
/// <returns>result params with job id and control id</returns>
public ServiceParameters SubmitRequest(IList <ISequence> sequence, ClustalWParameters parameters)
{
ServiceParameters result = new ServiceParameters();
if (null == sequence)
{
throw new ArgumentNullException("Sequence");
}
if (null == parameters)
{
throw new ArgumentNullException("Parameters");
}
// ClusterOption = biosim cbsum1 cbsum2k8 cbsusrv05 cbsum2 or Auto
string[] output = _baseClient.CreateJob(tAppId.P_CLUSTALW, "test_BioHPC_Job", "1", parameters.Values[ClustalWParameters.Email].ToString(),
string.Empty, parameters.Values[ClustalWParameters.ClusterOption].ToString());
if (!output[0].Contains(ERROR))
{
result.JobId = output[1];
result.Parameters.Add(CONTROLID, output[2]);
AppInputData inputData = _baseClient.InitializeApplicationParams(tAppId.P_CLUSTALW, "test_BioHPC_Job");
FastaFormatter formatter = new FastaFormatter();
StringBuilder inputSequence = new StringBuilder();
foreach (ISequence seq in sequence)
{
inputSequence.AppendLine(formatter.FormatString(seq));
}
//formatter.Format(sequence, "temp");
//StreamReader reader = new StreamReader("temp");
inputData.clustalw.inputsource = QuerySrcType.paste;
inputData.clustalw.inputstring = inputSequence.ToString();
inputData.clustalw.isDNA = false;
inputData.clustalw.action = (ClwActions)Enum.Parse(typeof(ClwActions),
parameters.Values[ClustalWParameters.ActionAlign].ToString());
inputData.clustalw.email_notify = true;
_baseClient.SubmitJob(result.JobId, result.Parameters[CONTROLID].ToString(), inputData);
result.Parameters.Add(SUBMISSONRESULT, SUCCESS);
// Only if the event is registered, invoke the thread
if (null != RequestCompleted)
{
// Start the BackGroundThread to check the status of job
_workerThread = new BackgroundWorker();
_workerThread.WorkerSupportsCancellation = true;
_workerThread.DoWork += new DoWorkEventHandler(ProcessRequestThread);
_workerThread.RunWorkerCompleted += new RunWorkerCompletedEventHandler(CompletedRequestThread);
_workerThread.RunWorkerAsync(result);
}
}
else
{
result.Parameters.Add(SUBMISSONRESULT, output[0]);
}
return(result);
}
/// <summary>
/// Submit the search request with the user supplied configuration parameters
/// and sequence. Implementation should make use of the MBF.IO formatters
/// to convert the sequence into the web interface compliant sequence format.
/// This method performs parameter validation and throw Exception on invalid input.
/// </summary>
/// <remarks>An exception is thrown if the request does not succeed.</remarks>
/// <param name="sequence">The sequence to search with</param>
/// <param name="parameters">Blast input parameters</param>
/// <returns>Request Identifier</returns>
public string SubmitRequest(ISequence sequence, BlastParameters parameters)
{
if (null != sequence)
{
FastaFormatter formatter = new FastaFormatter();
parameters.Add("Query", formatter.FormatString(sequence));
}
if (null == parameters)
{
throw new ArgumentNullException("parameters");
}
if (!string.IsNullOrEmpty(Configuration.EmailAddress))
{
if (!parameters.Settings.ContainsKey(PARAMETEREMAIL))
{
parameters.Add(PARAMETEREMAIL, Configuration.EmailAddress);
}
}
string requestIdentifier = string.Empty;
// Validate the Parameter
ParameterValidationResult valid = ValidateParameters(parameters);
if (!valid.IsValid)
{
throw new Exception(valid.ValidationErrors);
}
parameters.Add(PARAMETERCOMMAND, COMMANDPUT);
WebAccessor accessor = new WebAccessor();
WebAccessorResponse webAccessorResponse;
if (Configuration.UseBrowserProxy)
{
accessor.GetBrowserProxy();
}
webAccessorResponse = accessor.SubmitHttpRequest(
ServiceUri,
true, // do POST
parameters.Settings); // request parameters
if (!webAccessorResponse.IsSuccessful)
{
// failed
accessor.Close();
throw new Exception(String.Format(CultureInfo.InvariantCulture,
Resources.HTTPSUBMITFAILED,
webAccessorResponse.StatusDescription));
}
string info = ExtractInfoSection(webAccessorResponse.ResponseString);
if (!String.IsNullOrEmpty(info))
{
int ridStart = info.IndexOf("RID = ", StringComparison.OrdinalIgnoreCase);
if (ridStart >= 0)
{
ridStart += "RID = ".Length;
int ridEnd = info.IndexOf('\n', ridStart);
if (ridEnd >= 0)
{
requestIdentifier = info.Substring(ridStart, ridEnd - ridStart);
}
}
}
accessor.Close();
if (string.IsNullOrEmpty(requestIdentifier))
{
string message = String.Format(CultureInfo.InvariantCulture,
Resources.RIDEXTRACTFAILED,
ExtractError(webAccessorResponse.ResponseString));
throw new Exception(message);
}
// Only if the event is registered, invoke the thread
if (null != RequestCompleted)
{
ThreadParameter threadParameter = new ThreadParameter(
requestIdentifier,
sequence,
parameters);
// Start the BackGroundThread to check the status of job
_workerThread = new BackgroundWorker();
_workerThread.WorkerSupportsCancellation = true;
_workerThread.DoWork += new DoWorkEventHandler(ProcessRequestThread);
_workerThread.RunWorkerCompleted += new RunWorkerCompletedEventHandler(CompletedRequestThread);
_workerThread.RunWorkerAsync(threadParameter);
}
return(requestIdentifier);
}
