/// <summary>
/// When implemented in a derived class, performs the execution of the activity.
/// </summary>
/// <param name="context">The execution context under which the activity executes.</param>
protected override void Execute(CodeActivityContext context)
{
string filename = Filename.Get(context);
ISequenceFormatter formatter = SequenceFormatters.FindFormatterByFileName(filename);
if (formatter == null)
{
throw new ArgumentException("Could not determine formatter for " + filename);
}
if (LogOutput)
{
var tw = context.GetExtension <TextWriter>() ?? Console.Out;
tw.WriteLine("Writing sequences to " + filename);
}
try
{
foreach (var s in Sequences.Get(context))
{
formatter.Format(s);
}
}
finally
{
formatter.Close();
}
}
/// <summary>
/// When implemented in a derived class and using the specified execution context, callback method, and user state, enqueues an asynchronous activity in a run-time workflow.
/// </summary>
/// <returns>
/// An object.
/// </returns>
/// <param name="context">Information that defines the execution environment for the <see cref="T:System.Activities.AsyncCodeActivity"/>.</param><param name="callback">The method to be called after the asynchronous activity and completion notification have occurred.</param><param name="state">An object that saves variable information for an instance of an asynchronous activity.</param>
protected override IAsyncResult BeginExecute(AsyncCodeActivityContext context, AsyncCallback callback, object state)
{
NcbiBlastWebHandler service = new NcbiBlastWebHandler();
// fill in the BLAST settings:
var searchParams = new BlastRequestParameters
{
Program = Program.Get(context) ?? DefaultProgram,
Database = Database.Get(context) ?? DefaultDatabase
};
searchParams.ExtraParameters.Add("Expect", "1e-10");
searchParams.Sequences.AddRange(Sequences.Get(context));
// Create the request
var runningTask = service.ExecuteAsync(searchParams, CancellationToken.None);
context.UserState = runningTask;
return(runningTask.AsApm(callback, state));
}
/// <summary>
/// When implemented in a derived class, performs the execution of the activity.
/// </summary>
/// <returns>
/// The result of the activity’s execution.
/// </returns>
/// <param name="context">The execution context under which the activity executes.</param>
protected override IDeNovoAssembly Execute(CodeActivityContext context)
{
// Setup the aligner to use
string alignerName = (AlignerName ?? DefaultAligner).ToLowerInvariant();
var aligner = SequenceAligners.All.FirstOrDefault(sa => sa.Name.ToLowerInvariant() == alignerName);
if (aligner == null)
{
throw new ArgumentException("Could not find aligner: " + alignerName);
}
aligner.GapOpenCost = GapOpenCost;
aligner.GapExtensionCost = GapExtensionCost;
var smName = SimilarityMatrix ?? DefaultMatrix;
SimilarityMatrix.StandardSimilarityMatrix sm;
if (Enum.TryParse(smName, true, out sm))
{
aligner.SimilarityMatrix = new SimilarityMatrix(sm);
}
// Create the assembler
OverlapDeNovoAssembler assembler = new OverlapDeNovoAssembler
{
AssumeStandardOrientation = this.AssumeStandardOrientation,
MergeThreshold = this.MergeThreshold,
OverlapAlgorithm = aligner
};
var consensus = assembler.Assemble(Sequences.Get(context));
Contigs.Set(context, ((IOverlapDeNovoAssembly)consensus).Contigs);
return(consensus);
}
