/// <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 InputParameters GetRequestParameter(
BlastParameters parameters)
{
InputParameters blastParameter = new InputParameters();
// check required parameters:
if (parameters.Settings[ParameterDatabase].Contains(","))
{
blastParameter.database = parameters.Settings[ParameterDatabase].Split(",".ToCharArray());
}
else
{
blastParameter.database = new string[1];
blastParameter.database[0] = parameters.Settings[ParameterDatabase];
}
// force program to lowercase, per EBI docs (though the service seems
// to work fine regardless of the case of this parameter)
blastParameter.program = parameters.Settings[ParameterProgram].ToLower(CultureInfo.CurrentCulture);
// set the sequence Type.
blastParameter.stype = parameters.Settings[ParameterSequenceType].ToLower(CultureInfo.CurrentCulture);
// Set the Alignment View property.
if (parameters.Settings.ContainsKey(ParameterAlignmentView))
{
blastParameter.align = (int?)int.Parse(parameters.Settings[ParameterAlignmentView]);
blastParameter.alignSpecified = true;
}
else
{
blastParameter.align = int.Parse(BlastParameters.Parameters[ParameterKeyAlignmentView].DefaultValue);
blastParameter.alignSpecified = true;
}
//// 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.alignments = (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 = parameters.Settings[ParameterExpect];
}
return(blastParameter);
}
/// <remarks/>
public void runAsync(string email, string title, InputParameters parameters)
{
this.runAsync(email, title, parameters, null);
}
/// <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
/// </summary>
/// <remarks>An exception is thrown if the request does not succeed.</remarks>
/// <param name="sequences">List of sequence to search with</param>
/// <param name="parameters">Blast input parameters</param>
/// <returns>Request Identifier</returns>
public string SubmitRequest(IList <ISequence> sequences, BlastParameters parameters)
{
string emailAddress = string.Empty;
if (null == sequences)
{
throw new ArgumentNullException("sequences");
}
if (null == parameters)
{
throw new ArgumentNullException("parameters");
}
string tempEmail;
if (parameters.Settings.TryGetValue(ParameterEmail, out tempEmail) &&
!string.IsNullOrEmpty(tempEmail))
{
emailAddress = tempEmail;
}
string requestIdentifier = string.Empty;
// Validate the Parameter
ParameterValidationResult valid = ValidateParameters(parameters);
if (!valid.IsValid)
{
throw new Exception(valid.ValidationErrors);
}
// Submit the job to server
InputParameters blastRequest = GetRequestParameter(parameters);
StringBuilder seqBuilder = new StringBuilder();
foreach (ISequence sequence in sequences)
{
byte[] buffer = new byte[80];
int bufferIndex = 0, maxLineSize = 80;
seqBuilder.AppendLine(">" + sequence.ID);
for (long index = 0; index < sequence.Count; index += maxLineSize)
{
for (bufferIndex = 0; bufferIndex < maxLineSize && index + bufferIndex < sequence.Count; bufferIndex++)
{
buffer[bufferIndex] = sequence[index + bufferIndex];
}
string line = ASCIIEncoding.ASCII.GetString(buffer, 0, bufferIndex);
seqBuilder.AppendLine(line);
}
}
blastRequest.sequence = seqBuilder.ToString();
requestIdentifier = blastClient.run(emailAddress, string.Empty, blastRequest);
// Only if the event is registered, invoke the thread
if (null != RequestCompleted)
{
BlastThreadParameter threadParameter = new BlastThreadParameter(
requestIdentifier,
null,
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);
}
public string run([System.Xml.Serialization.XmlElementAttribute(Form = System.Xml.Schema.XmlSchemaForm.Unqualified)] string email, [System.Xml.Serialization.XmlElementAttribute(Form = System.Xml.Schema.XmlSchemaForm.Unqualified, IsNullable = true)] string title, [System.Xml.Serialization.XmlElementAttribute(Form = System.Xml.Schema.XmlSchemaForm.Unqualified)] InputParameters parameters)
{
object[] results = this.Invoke("run", new object[] {
email,
title,
parameters
});
return((string)(results[0]));
}
