/// <summary>
/// Submit the search request with the user supplied configuration parameters
/// and sequence. Implementation should make use of the Bio.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)
{
throw new ArgumentNullException("sequence");
}
if (null == parameters)
{
throw new ArgumentNullException("parameters");
}
string requestIdentifier = string.Empty;
// Validate the Parameter
ParameterValidationResult valid = ValidateParameters(parameters);
if (!valid.IsValid)
{
throw new Exception(valid.ValidationErrors);
}
// Submit the job to server
inputParams blastRequest = GetRequestParameter(
sequence,
parameters);
blastRequest.appxml = APPXMLYES;
blastRequest.async = true;
data[] mydata = new data[1];
mydata[0] = new data();
mydata[0].type = SEQUENCETYPE;
mydata[0].content = sequence.ToString();
requestIdentifier = _blastClient.runWUBlast(blastRequest, mydata);
// 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);
}
/// <summary>
/// Get the blast service request object with all the request parameter set
/// </summary>
/// <param name="sequence">Input sequece</param>
/// <param name="parameters">Blast parameters</param>
/// <returns>Blast service request object</returns>
private static inputParams GetRequestParameter(
ISequence sequence,
BlastParameters parameters)
{
inputParams blastParameter = new inputParams();
// check required parameters:
blastParameter.database = parameters.Settings[PARAMETERDATABASE];
// force program to uppercase, per EBI docs (though the service seems
// to work fine regardless of the case of this parameter)
blastParameter.program = parameters.Settings[PARAMETERPROGRAM].ToUpper();
// note: query is not part of the inputParams class, so the caller will
// need to handle it separately.
blastParameter.email = parameters.Settings[PARAMETEREMAIL];
// apply any addition validation logic and set remaining supported parameters:
// validate filters here, since QBLAST uses a different set:
if (parameters.Settings.ContainsKey(PARAMETERFILTER))
{
blastParameter.filter = parameters.Settings[PARAMETERFILTER];
}
if (parameters.Settings.ContainsKey(PARAMETERALIGNMENTS))
{
blastParameter.numal = (int?)int.Parse(parameters.Settings[PARAMETERALIGNMENTS]);
}
if (parameters.Settings.ContainsKey(PARAMETERMATRIXNAME))
{
blastParameter.matrix = parameters.Settings[PARAMETERMATRIXNAME];
}
if (parameters.Settings.ContainsKey(PARAMETEREXPECT))
{
blastParameter.exp = (float?)float.Parse(parameters.Settings[PARAMETEREXPECT]);
}
return(blastParameter);
}
/// <summary>
/// Get the blast service request object with all the request parameter set
/// </summary>
/// <param name="parameters">Blast parameters</param>
/// <returns>Blast service request object</returns>
private static inputParams GetRequestParameter(
BlastParameters parameters)
{
inputParams blastParameter = new inputParams();
// check required parameters:
blastParameter.database = parameters.Settings[ParameterDatabase];
// force program to uppercase, per EBI docs (though the service seems
// to work fine regardless of the case of this parameter)
blastParameter.program = parameters.Settings[ParameterProgram].ToUpperInvariant();
// note: query is not part of the inputParams class, so the caller will
// need to handle it separately.
blastParameter.email = parameters.Settings[ParameterEmail];
// apply any addition validation logic and set remaining supported parameters:
// validate filters here, since QBLAST uses a different set:
if (parameters.Settings.ContainsKey(ParameterFilter))
{
blastParameter.filter = parameters.Settings[ParameterFilter];
}
if (parameters.Settings.ContainsKey(ParameterAlignments))
{
blastParameter.numal = (int?)int.Parse(parameters.Settings[ParameterAlignments], CultureInfo.InvariantCulture);
}
if (parameters.Settings.ContainsKey(ParameterMatrixName))
{
blastParameter.matrix = parameters.Settings[ParameterMatrixName];
}
if (parameters.Settings.ContainsKey(ParameterExpect))
{
blastParameter.exp = (float?)float.Parse(parameters.Settings[ParameterExpect], CultureInfo.InvariantCulture);
}
return(blastParameter);
}
/// <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)
{
throw new ArgumentNullException("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);
}
// Submit the job to server
inputParams blastRequest = GetRequestParameter(parameters);
blastRequest.appxml = AppXmlYes;
blastRequest.async = true;
data[] mydata = new data[1];
mydata[0] = new data();
mydata[0].type = SequenceType;
FastaFormatter formatter = new FastaFormatter();
mydata[0].content = formatter.FormatString(sequence);
requestIdentifier = _blastClient.runWUBlast(blastRequest, mydata);
// 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);
}
