/// <summary>
/// This method validates the gap cost input
/// and on success adds the gap cost to the service parameters
/// </summary>
/// <param name="serviceParam">service param to add the param</param>
/// <returns>whether the gap cost was valid and added or not</returns>
private bool CheckNAddGapCostField(ref BlastRequestParameters serviceParam)
{
int number;
if (!Int32.TryParse(this.gapOpenTxt.Text, out number) && number != 0)
{
MessageBox.Show(
Properties.Resources.INVALID_TEXT + GAPCOSTS + Properties.Resources.VALUE_TEXT,
Properties.Resources.CAPTION,
MessageBoxButton.OK,
MessageBoxImage.Error);
return(false);
}
if (!Int32.TryParse(this.gapOpenTxt.Text, out number) && number != 0)
{
MessageBox.Show(
Properties.Resources.INVALID_TEXT + GAPCOSTS + Properties.Resources.VALUE_TEXT,
Properties.Resources.CAPTION,
MessageBoxButton.OK,
MessageBoxImage.Error);
return(false);
}
serviceParam.ExtraParameters.Add(GAPCOSTS, this.gapOpenTxt.Text + " " + this.gapExtendedTxt.Text);
return(true);
}
/// <summary>
/// This method would add service params to the given service param,
/// The would get all the children items from the stack panel and would read the param values
/// and add to the search service parameters.
/// </summary>
/// <param name="serviceParam">Service parameter</param>
/// <param name="panel">Stack panel</param>
/// <returns>returns whether the given param was added or not</returns>
private bool AddServiceParams(ref BlastRequestParameters serviceParam, StackPanel panel)
{
bool valid = true;
foreach (UIElement element in panel.Children)
{
var txtBox = element as TextBox;
var lstBox = element as ListBox;
var chkbox = element as CheckBox;
if (txtBox != null)
{
valid = AddValidServiceParams(ref serviceParam, txtBox.Tag.ToString(), txtBox.Text);
}
else if (lstBox != null)
{
}
else if (chkbox != null)
{
}
else
{
var combo = element as ComboBox;
if (combo != null && combo.Visibility == Visibility.Visible)
{
valid = AddValidServiceParams(
ref serviceParam,
combo.Tag.ToString(),
combo.SelectedValue.ToString());
}
}
if (!valid)
{
break;
}
}
// checks the gap cost field
if (valid)
{
valid = this.CheckNAddGapCostField(ref serviceParam);
}
return(valid);
}
public async Task <string> SearchBlast(string seqString, CancellationToken cancellationToken)
{
NcbiBlastWebHandler handler = new NcbiBlastWebHandler()
{
LogOutput = Log,
EndPoint = "https://www.ncbi.nlm.nih.gov/blast/Blast.cgi",
TimeoutInSeconds = 3600
};
string cleanDNASequence = new string(seqString.Where(c => c == 'A' || c == 'G' || c == 'T' || c == 'C').ToArray());
Sequence sequence = new Sequence(DnaAlphabet.Instance, cleanDNASequence);
List <Bio.ISequence> sequences = new List <Bio.ISequence>();
sequences.Append(sequence);
var request = new BlastRequestParameters(sequences)
{
Database = "nt",
Program = BlastProgram.Blastn
};
request.Sequences.Add(sequence);
HttpContent result = handler.BuildRequest(request);
var executeResult = await handler.ExecuteAsync(request, cancellationToken);
if (executeResult == null)
{
return("Your sequence is not found (hits=0)");
}
//Stream stream = await result.ReadAsStreamAsync();
Bio.Web.Blast.BlastXmlParser parser = new BlastXmlParser();
var results = parser.Parse(executeResult).ToList();
var resString = String.Join(Environment.NewLine,
results.FirstOrDefault()
.Records.FirstOrDefault()
.Hits.Take(5)
.Select(x => $"ID: {x.Id}, Accession: {x.Accession}, Def: {x.Def}")
.ToArray());
return(resString);
}
/// <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>
/// This event is fired on click of the submit button on the dialog,
/// this would validate the parameters accordingly and on success would initiate adding
/// of the parameters to the given service parameters
/// </summary>
/// <param name="sender">submit button</param>
/// <param name="e">Event Data</param>
private void OnBtnSubmitClick(object sender, RoutedEventArgs e)
{
var serviceParam = new BlastRequestParameters();
bool valid = this.AddServiceParams(ref serviceParam, this.firstStk);
if (valid)
{
valid = this.AddServiceParams(ref serviceParam, this.secondStk);
}
if (valid)
{
valid = this.AddServiceParams(ref serviceParam, this.thirdColumnParams);
}
if (valid)
{
valid = this.AddServiceParams(ref serviceParam, this.commonParamsStk);
}
if (valid && this.serviceParams.Visibility == Visibility.Visible)
{
valid = this.AddServiceParams(ref serviceParam, this.serviceParams);
}
if (valid)
{
var args = new WebServiceInputEventArgs(this.serviceName, serviceParam);
this.WebServiceInputArgs = args;
if (this.ExecuteSearch != null)
{
this.ExecuteSearch.Invoke(this, args);
this.Close();
}
else
{
this.Close();
}
}
}
/// <summary>
/// Initializes a new instance of the WebServiceInputEventArgs class
/// </summary>
/// <param name="serviceName">Web service name</param>
/// <param name="parameters">the selected service parameters</param>
public WebServiceInputEventArgs(string serviceName, BlastRequestParameters parameters)
{
this.ServiceName = serviceName;
this.Parameters = parameters;
}
/// <summary>
/// This method would validate and add the params to the service
/// parameters for the requested search
/// </summary>
/// <param name="serviceParam">Service parameter</param>
/// <param name="paramName">Param name</param>
/// <param name="paramValue">Param value</param>
/// <returns>whether the parameter was valid</returns>
private static bool AddValidServiceParams(ref BlastRequestParameters serviceParam, string paramName, string paramValue)
{
return(false);
}
