protected TopDownIqTarget CreateParentTarget(List <List <string> > processedGroup)
{
var target = new TopDownIqTarget();
var parser = new IqCodeParser();
target.DatabaseReference = ParseStringField(processedGroup[0], ProteinNameHeader);
target.Code = ParseStringField(processedGroup[0], PeptideHeader);
target.EmpiricalFormula = parser.GetEmpiricalFormulaFromSequence(target.Code);
target.PTMList = parser.GetPTMList(target.Code);
target.MonoMassTheor = ParseDoubleField(processedGroup[0], AdjustedPrecursorMassHeader);
var children = new List <IqTarget>();
foreach (var line in processedGroup)
{
children.Add(ConvertTextToIqTarget(line));
}
target.AddTargetRange(children);
return(target);
}
/// <summary>
/// Combines charge state results into one line for target level output
/// </summary>
/// <param name="results"></param>
/// <param name="includeHeader"></param>
/// <returns></returns>
public string GetTargetResultAsString(IEnumerable <IqResult> results, bool includeHeader = false)
{
var sb = new StringBuilder();
if (includeHeader)
{
var header = GetHeader();
sb.Append(header);
sb.Append(Environment.NewLine);
}
double abundance = 0, correlationMedian = 0;
var chargeStateList = "";
var fitScoreList = new List <double>();
var isFirst = true;
IqTarget target = new TopDownIqTarget();
foreach (var result in results)
{
//Sums abundance from each result
abundance += result.Abundance;
//Eliminates charge 0 or targets that are too poor to quantify
if (!(result.Target.ChargeState == 0 || result.Abundance <= 0))
{
fitScoreList.Add(result.FitScore);
if (isFirst)
{
chargeStateList += (result.Target.ChargeState);
isFirst = false;
}
else
{
chargeStateList += (", " + result.Target.ChargeState);
}
}
//Looks for parent level target for information
var parentResult = result as TopDownIqResult;
if (parentResult != null)
{
target = parentResult.Target;
correlationMedian = parentResult.SelectedCorrelationGroup.ChargeCorrelationMedian();
}
}
double medianFit = 1;
if (fitScoreList.Count != 0)
{
medianFit = MathUtils.GetMedian(fitScoreList);
}
sb.Append(target.ID);
sb.Append(Delimiter);
sb.Append(target.Code);
sb.Append(Delimiter);
sb.Append(target.EmpiricalFormula);
sb.Append(Delimiter);
sb.Append(target.MonoMassTheor);
sb.Append(Delimiter);
sb.Append(chargeStateList);
sb.Append(Delimiter);
sb.Append(abundance);
sb.Append(Delimiter);
sb.Append(medianFit);
sb.Append(Delimiter);
sb.Append(correlationMedian);
var outString = sb.ToString();
return(outString);
}
