/// <summary>
/// Determines if the target should be filtered or not.
/// </summary>
/// <param name="t"></param>
/// <returns></returns>
public bool ShouldFilter(Target t)
{
// This is a bad way to do this...but
// I don't want to put the immediate effort into redesigning this...more work
// is needed to segment out the options class out of a general options class and into
// a concrete class or classes
SequestResult sequest = t as SequestResult;
if (sequest != null)
{
// If it is to be exported, then we should not filter it
return(!IsToBeExported(sequest));
}
XTandemResult xtandem = t as XTandemResult;
if (xtandem != null)
{
return(!IsToBeExported(xtandem));
}
MsgfPlusResult msgfResult = t as MsgfPlusResult;
if (msgfResult != null)
{
return(!IsToBeExported(msgfResult));
}
return(true);
}
/// <summary>
/// Determines if a feature should be filtered or not.
/// </summary>
/// <param name="t"></param>
/// <returns></returns>
public bool ShouldFilter(Target target)
{
Sequence sequence = target.SequenceData;
if (sequence == null)
{
return(true);
}
// in the alignment we will only use the unmodified peptides
if (sequence.ModificationCount > Options.MaxModificationsForAlignment)
{
return(true);
}
SequestResult result = target as SequestResult;
if (result == null)
{
return(true);
}
if (result.XCorr < Options.MinXCorrForAlignment)
{
return(true);
}
return(false);
}
public bool IsToBeExported(SequestResult seqResult)
{
short charge = seqResult.Charge;
if (charge > SequestResult.MAX_CHARGE_FOR_FSCORE)
{
charge = SequestResult.MAX_CHARGE_FOR_FSCORE;
}
if (seqResult.NumTrypticEnds == 2)
{
if (!ExportTryptic)
{
return(false);
}
if (UseDelCN && seqResult.DelCn > MaxDelCN)
{
return(false);
}
if (seqResult.XCorr >= marrXCorrForExportTryptic[charge - 1])
{
return(true);
}
else
{
return(false);
}
}
if (seqResult.NumTrypticEnds == 1)
{
if (!ExportPartiallyTryptic)
{
return(false);
}
if (UseDelCN && seqResult.DelCn > MaxDelCN)
{
return(false);
}
if (seqResult.XCorr >= marrXCorrForExportPartiallyTryptic[charge - 1])
{
return(true);
}
else
{
return(false);
}
}
if (seqResult.NumTrypticEnds == 0)
{
if (!ExportNonTryptic)
{
return(false);
}
if (UseDelCN && seqResult.DelCn > MaxDelCN)
{
return(false);
}
if (seqResult.XCorr >= marrXCorrForExportNonTryptic[charge - 1])
{
return(true);
}
else
{
return(false);
}
}
return(false);
}
/// <summary>
/// Read and process a Sequest PHRP file
/// </summary>
/// <param name="path">Sequest file to read</param>
/// <returns></returns>
public override LcmsDataSet Read(string path)
{
var results = new List <SequestResult>();
var filter = new SequestTargetFilter(ReaderOptions);
// Get the Evidences using PHRPReader which looks at the path that was passed in to determine the data type
int resultsProcessed = 0;
var reader = InitializeReader(path);
while (reader.MoveNext())
{
resultsProcessed++;
if (resultsProcessed % 500 == 0)
{
UpdateProgress(reader.PercentComplete, "Reading peptides");
}
if (AbortRequested)
{
break;
}
// Skip this PSM if it doesn't pass the import filters
double xcorr = reader.CurrentPSM.GetScoreDbl(clsPHRPParserSequest.DATA_COLUMN_XCorr, 0);
double specProb = 0;
if (!string.IsNullOrEmpty(reader.CurrentPSM.MSGFSpecProb))
{
specProb = Convert.ToDouble(reader.CurrentPSM.MSGFSpecProb);
}
if (filter.ShouldFilter(xcorr, specProb))
{
continue;
}
reader.FinalizeCurrentPSM();
if (reader.CurrentPSM.SeqID == 0)
{
continue;
}
var result = new SequestResult
{
AnalysisId = reader.CurrentPSM.ResultID
};
StorePsmData(result, reader, specProb);
StoreDatasetInfo(result, reader, path);
// Populate items specific to Sequest
result.Reference = reader.CurrentPSM.ProteinFirst;
result.NumTrypticEnds = reader.CurrentPSM.NumTrypticTerminii;
result.DelCn = reader.CurrentPSM.GetScoreDbl(clsPHRPParserSequest.DATA_COLUMN_DelCn, 0);
result.DelCn2 = reader.CurrentPSM.GetScoreDbl(clsPHRPParserSequest.DATA_COLUMN_DelCn2, 0);
result.RankSp = (short)reader.CurrentPSM.GetScoreInt(clsPHRPParserSequest.DATA_COLUMN_RankSp, 0);
result.RankXc = (short)reader.CurrentPSM.GetScoreInt(clsPHRPParserSequest.DATA_COLUMN_RankXc, 0);
result.Sp = reader.CurrentPSM.GetScoreDbl(clsPHRPParserSequest.DATA_COLUMN_Sp, 0);
result.XCorr = xcorr;
result.DiscriminantValue = xcorr;
result.XcRatio = reader.CurrentPSM.GetScoreDbl(clsPHRPParserSequest.DATA_COLUMN_XcRatio, 0);
result.FScore = SequestResult.CalculatePeptideProphetDiscriminantScore(result);
results.Add(result);
}
ComputeNets(results);
return(new LcmsDataSet(Path.GetFileNameWithoutExtension(path), LcmsIdentificationTool.Sequest, results));
}
