/// <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);
}
XTandemResult result = target as XTandemResult;
if (result == null)
{
return(true);
}
if (result.LogPeptideEValue > Options.MaxLogEValForXTandemAlignment)
{
return(true);
}
return(false);
}
public bool IsToBeExported(XTandemResult xtResult)
{
if (xtResult.LogPeptideEValue > MaxLogEValForXTandemExport)
{
return(false);
}
if (xtResult.TrypticState == 2)
{
if (!ExportTryptic)
{
return(false);
}
else
{
return(true);
}
}
if (xtResult.TrypticState == 1)
{
if (!ExportPartiallyTryptic)
{
return(false);
}
else
{
return(true);
}
}
if (xtResult.TrypticState == 0)
{
if (!ExportNonTryptic)
{
return(false);
}
else
{
return(true);
}
}
return(false);
}
/// <summary>
/// Read and process a XTandem PHRP file
/// </summary>
/// <param name="path">XTandem file to read</param>
/// <returns></returns>
public override LcmsDataSet Read(string path)
{
var results = new List <XTandemResult>();
var filter = new XTandemTargetFilter(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 logPepEValue = reader.CurrentPSM.GetScoreDbl(clsPHRPParserXTandem.DATA_COLUMN_Peptide_Expectation_Value_LogE, 0);
double specProb = 0;
if (!string.IsNullOrEmpty(reader.CurrentPSM.MSGFSpecProb))
{
specProb = Convert.ToDouble(reader.CurrentPSM.MSGFSpecProb);
}
if (filter.ShouldFilter(logPepEValue, specProb))
{
continue;
}
reader.FinalizeCurrentPSM();
if (reader.CurrentPSM.SeqID == 0)
{
continue;
}
var result = new XTandemResult
{
AnalysisId = reader.CurrentPSM.ResultID
};
StorePsmData(result, reader, specProb);
StoreDatasetInfo(result, reader, path);
result.DataSet.Tool = LcmsIdentificationTool.XTandem;
// Populate items specific to X!Tandem
result.NumTrypticEnds = reader.CurrentPSM.NumTrypticTerminii;
result.BScore = reader.CurrentPSM.GetScoreDbl(clsPHRPParserXTandem.DATA_COLUMN_b_score, 0);
result.DeltaCn2 = reader.CurrentPSM.GetScoreDbl(clsPHRPParserXTandem.DATA_COLUMN_DeltaCn2, 0);
result.LogIntensity = reader.CurrentPSM.GetScoreDbl(clsPHRPParserXTandem.DATA_COLUMN_Peptide_Intensity_LogI, 0);
result.LogPeptideEValue = logPepEValue;
result.DiscriminantValue = logPepEValue;
result.NumberBIons = (short)reader.CurrentPSM.GetScoreInt(clsPHRPParserXTandem.DATA_COLUMN_b_ions);
result.NumberYIons = (short)reader.CurrentPSM.GetScoreInt(clsPHRPParserXTandem.DATA_COLUMN_y_ions);
result.PeptideHyperscore = reader.CurrentPSM.GetScoreDbl(clsPHRPParserXTandem.DATA_COLUMN_Peptide_Hyperscore, 0);
result.YScore = reader.CurrentPSM.GetScoreDbl(clsPHRPParserXTandem.DATA_COLUMN_y_score, 0);
results.Add(result);
}
ComputeNets(results);
return(new LcmsDataSet(Path.GetFileNameWithoutExtension(path), LcmsIdentificationTool.XTandem, results));
}
