/// <summary>
/// Configure and return the appropriate target filter
/// </summary>
/// <param name="tool"></param>
/// <param name="options"></param>
/// <returns></returns>
public static ITargetFilter Create(LcmsIdentificationTool tool, Options options)
{
ITargetFilter targetFilter = null;
switch (tool)
{
case LcmsIdentificationTool.MsgfPlus:
targetFilter = new MsgfPlusTargetFilter(options);
break;
case LcmsIdentificationTool.MZIdentML:
targetFilter = new MsgfPlusTargetFilter(options);
break;
case LcmsIdentificationTool.Sequest:
targetFilter = new SequestTargetFilter(options);
break;
case LcmsIdentificationTool.XTandem:
targetFilter = new XTandemTargetFilter(options);
break;
case LcmsIdentificationTool.MSAlign:
targetFilter = new MsAlignTargetFilter(options);
break;
}
return(targetFilter);
}
/// <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));
}
