/// <summary>
/// This method renders the single line report for BLAST hits.
/// </summary>
/// <param name="results">BLAST hits</param>
private void RenderSingleLineReport(IList <BlastResult> results, IBlastWebHandler blastService, string databaseName)
{
this.lstSingleLineReport.ItemsSource = null;
this.lstSingleLineReport.Items.Clear();
this.blastResultCollator.Clear();
this.Focus();
foreach (BlastResult result in results)
{
foreach (BlastSearchRecord record in result.Records)
{
if (null != record.Hits &&
0 < record.Hits.Count)
{
foreach (Hit hit in record.Hits)
{
if (null != hit.Hsps &&
0 < hit.Hsps.Count)
{
foreach (Hsp hsp in hit.Hsps)
{
BlastResultCollator blast = new BlastResultCollator();
blast.Uri = BlastHitUrlResolver.ResolveUrl(hit.Id, blastService, databaseName);
blast.Alignment = hsp.AlignmentLength;
blast.Bit = hsp.BitScore;
blast.EValue = hsp.EValue;
blast.Identity = hsp.IdentitiesCount;
blast.Length = hit.Length;
blast.QEnd = hsp.QueryEnd;
blast.QStart = hsp.QueryStart;
blast.QueryId = record.IterationQueryId;
blast.SEnd = hsp.HitEnd;
blast.SStart = hsp.HitStart;
blast.SubjectId = hit.Id;
blast.Positives = hsp.PositivesCount;
blast.QueryString = hsp.QuerySequence;
blast.SubjectString = hsp.HitSequence;
blast.Accession = hit.Accession;
blast.Description = hit.Def;
blast.Gaps = hsp.Gaps;
this.blastResultCollator.Add(blast);
}
}
}
}
}
}
this.lstSingleLineReport.ItemsSource = this.blastResultCollator;
// Invoke the Silvermap
if (this.blastResultCollator.Count > 0 || this.webServiceReportTab.SelectedIndex == 1)
{
this.silverMapControl.InvokeSilverMap(this.blastResultCollator);
}
}
/// <summary>
/// This method displays BLAST hits on the UI.
/// </summary>
/// <param name="results">BLAST hits</param>
public void DisplayWebServiceOutput(IList <BlastResult> results, IBlastWebHandler blastService, string databaseName)
{
if (results != null && results.Count >= 1)
{
this.RenderSingleLineReport(results, blastService, databaseName);
this.blastResult = results[0];
this.txtDate.Text = DateTime.Now.Date.ToString(CultureInfo.CurrentCulture);
this.txtDataBaseName.Text = this.blastResult.Metadata.Database;
this.txtVersion.Text = this.blastResult.Metadata.Version;
}
}
/// <summary>
/// Get the url for a blast hit
/// </summary>
/// <param name="hitID">Blast hit id</param>
/// <param name="blastService">Instance of the blast service</param>
/// <param name="databaseName">Database name used in the blast query</param>
/// <returns>A url if resolved, else null</returns>
public static string ResolveUrl(string hitID, IBlastWebHandler blastService, string databaseName)
{
// NCBI
if (blastService.Name == WebServices.NcbiBlast.Name)
{
string[] idSplit = hitID.Split('|');
if (idSplit.Length < 2)
{
return(null);
}
string id = idSplit[1];
return(string.Format("http://www.ncbi.nlm.nih.gov/protein/{0}", id));
}
// TODO:
/*
* // EBI
* else if (blastService.Name == WebServices.EbiBlast.Name)
* {
* string[] idSplit = hitID.Split(':', ';');
* if (idSplit.Length < 2)
* return null;
*
* string id = idSplit[1];
*
* switch(databaseName)
* {
* case "em_rel":
* return string.Format("http://www.ebi.ac.uk/ena/data/view/{0}", id);
*
* case "uniprot":
* return string.Format("http://www.uniprot.org/uniprot/{0}.html", id);
*
* default:
* return null;
* }
* }
*/
// Return null if url was not resolved
return(null);
}
