/// <summary>
/// Get all the key=value pairs (pins) exposed by the implementor.
/// </summary>
/// <param name="item">The optional item. The item with its parts
/// can optionally be passed to this method for those parts requiring
/// to access further data.</param>
/// <returns>The pins.</returns>
public override IEnumerable <DataPin> GetDataPins(IItem item)
{
DataPinBuilder builder = new DataPinBuilder(
new StandardDataPinTextFilter());
builder.AddValue("id", GraffitiId);
if (!string.IsNullOrEmpty(Language))
{
builder.AddValue("language", Language);
}
if (!string.IsNullOrEmpty(Verse))
{
builder.AddValue("verse", Verse);
}
if (!string.IsNullOrEmpty(Author))
{
builder.AddValue("author", Author, filter: true, filterOptions: true);
}
if (Identifications?.Count > 0)
{
builder.AddValues("pid", Identifications.Select(i => i.Id));
}
if (Date != null)
{
builder.AddValue("date-value", Date.GetSortValue());
}
return(builder.Build(this));
}
public override string ToString()
{
StringBuilder sb = new StringBuilder();
sb.Append(SpectraFileInfo.FilenameWithoutExtension + "\t");
sb.Append(string.Join("|", Identifications.Select(p => p.BaseSequence).Distinct()) + '\t');
sb.Append(string.Join("|", Identifications.Select(p => p.ModifiedSequence).Distinct()) + '\t');
var t = Identifications.SelectMany(p => p.ProteinGroups.Select(v => v.ProteinGroupName)).Distinct().OrderBy(p => p);
if (t.Any())
{
sb.Append(string.Join(";", t) + '\t');
}
else
{
sb.Append("" + '\t');
}
sb.Append("" + Identifications.First().MonoisotopicMass + '\t');
if (!IsMbrPeak)
{
sb.Append("" + Identifications.First().Ms2RetentionTimeInMinutes + '\t');
}
else
{
sb.Append("" + '\t');
}
sb.Append("" + Identifications.First().PrecursorChargeState + '\t');
sb.Append("" + ClassExtensions.ToMz(Identifications.First().MonoisotopicMass, Identifications.First().PrecursorChargeState) + '\t');
sb.Append("" + Intensity + "\t");
if (Apex != null)
{
sb.Append("" + IsotopicEnvelopes.Min(p => p.IndexedPeak.RetentionTime) + "\t");
sb.Append("" + Apex.IndexedPeak.RetentionTime + "\t");
sb.Append("" + IsotopicEnvelopes.Max(p => p.IndexedPeak.RetentionTime) + "\t");
sb.Append("" + Apex.IndexedPeak.Mz + "\t");
sb.Append("" + Apex.ChargeState + "\t");
}
else
{
sb.Append("" + "-" + "\t");
sb.Append("" + "-" + "\t");
sb.Append("" + "-" + "\t");
sb.Append("" + "-" + "\t");
sb.Append("" + "-" + "\t");
}
sb.Append("" + NumChargeStatesObserved + "\t");
if (IsMbrPeak)
{
sb.Append("" + "MBR" + "\t");
}
else
{
sb.Append("" + "MSMS" + "\t");
}
sb.Append("" + (IsMbrPeak ? MbrScore.ToString() : "") + "\t");
sb.Append("" + Identifications.Count + "\t");
sb.Append("" + NumIdentificationsByBaseSeq + "\t");
sb.Append("" + NumIdentificationsByFullSeq + "\t");
sb.Append("" + SplitRT + "\t");
sb.Append("" + MassError + "\t");
return(sb.ToString());
}
public void ResolveIdentifications()
{
this.NumIdentificationsByBaseSeq = Identifications.Select(v => v.BaseSequence).Distinct().Count();
this.NumIdentificationsByFullSeq = Identifications.Select(v => v.ModifiedSequence).Distinct().Count();
}
