public ReturnResultDTO ImportXmlData(List <ImportXMLDataDTO> inputDTOList)
{
int scanId = 0;
int subScnaID = 0;
ReturnResultDTO dtoItem;
if (inputDTOList.Any(c => c.IsAdditionalScan))
{
//Generate New ScanID;
scanId = inputDTOList.First().ScanId;
subScnaID = inputDTOList.First().SubScanId + 1;
}
//Create MasterScan
ScanMaster master = CreateScanMaster(scanId, subScnaID, inputDTOList.First().UserId, inputDTOList.First().ClientName, inputDTOList.First().ScanDate, inputDTOList.First().ScanName);
using (var context = new WebParser.DAL.DataModel.WebParserEntities())
{
if (!inputDTOList.Any(c => c.IsAdditionalScan))
{
ScanNumber newNumber = new ScanNumber()
{
UserId = inputDTOList.First().UserId
};
context.ScanNumbers.Add(newNumber);
context.SaveChanges();
var userID = inputDTOList.First().UserId;
var listOfScan = context.ScanNumbers.Where(c => c.UserId == userID).ToList();
scanId = listOfScan.Last().ScanId;
master.ScanId = scanId;
}
foreach (var item in inputDTOList)
{
CurrScan newItem = CreateCurrentScan(item, scanId, subScnaID);
master.CurrScans.Add(newItem);
//context.CurrScans.Add(newItem);
}
context.ScanMasters.Add(master);
int value = 0;
try
{
using (TransactionScope trans = new TransactionScope())
{
value = context.SaveChanges();
if (value > 0)
{
dtoItem = CheckExistingData(scanId);
dtoItem.IsSuccess = true;
trans.Complete();
}
else
{
dtoItem = new ReturnResultDTO();
dtoItem.IsSuccess = false;
trans.Dispose();
}
}
}
catch (Exception ex)
{
throw ex;
}
}
return(dtoItem);
}
public string ToString(IReadOnlyDictionary <string, int> ModstoWritePruned)
{
var sb = new StringBuilder();
sb.Append(Path.GetFileNameWithoutExtension(FullFilePath));
sb.Append('\t' + ScanNumber.ToString(CultureInfo.InvariantCulture));
sb.Append('\t' + ScanRetentionTime.ToString("F5", CultureInfo.InvariantCulture));
sb.Append('\t' + ScanExperimentalPeaks.ToString("F5", CultureInfo.InvariantCulture));
sb.Append('\t' + TotalIonCurrent.ToString("F5", CultureInfo.InvariantCulture));
sb.Append('\t' + (PrecursorScanNumber.HasValue ? PrecursorScanNumber.Value.ToString(CultureInfo.InvariantCulture) : "unknown"));
sb.Append('\t' + ScanPrecursorCharge.ToString("F5", CultureInfo.InvariantCulture));
sb.Append('\t' + ScanPrecursorMonoisotopicPeakMz.ToString("F5", CultureInfo.InvariantCulture));
sb.Append('\t' + ScanPrecursorMass.ToString("F5", CultureInfo.InvariantCulture));
sb.Append('\t' + Score.ToString("F3", CultureInfo.InvariantCulture));
sb.Append("\t" + Resolve(compactPeptides.Select(b => b.Value.Item1)).Item1); // Notch
sb.Append('\t' + NumDifferentCompactPeptides.ToString("F5", CultureInfo.InvariantCulture));
if (compactPeptides.First().Value.Item2 != null)
{
sb.Append("\t" + GlobalVariables.CheckLengthOfOutput(string.Join("|", compactPeptides.Select(b => b.Value.Item2.Count.ToString(CultureInfo.InvariantCulture)))));
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => b.BaseSequence)).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => b.Sequence)).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => b.EssentialSequence(ModstoWritePruned))).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => b.allModsOneIsNterminus)).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => string.Join("|", b.allModsOneIsNterminus.OrderBy(c => c.Key).Where(c => c.Value is ModificationWithMassAndCf).Select(c => (c.Value as ModificationWithMassAndCf).chemicalFormula.Formula)))).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => b.allModsOneIsNterminus.Select(c => (c.Value as ModificationWithMassAndCf)))).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => b.NumVariableMods)).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => b.MissedCleavages.HasValue ? b.MissedCleavages.Value.ToString(CultureInfo.InvariantCulture) : "unknown")).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => b.MonoisotopicMass)).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => ScanPrecursorMass - b.MonoisotopicMass)).Item1);
sb.Append('\t' + ResolveF2(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => ((ScanPrecursorMass - b.MonoisotopicMass) / b.MonoisotopicMass * 1e6))).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => b.Protein.Accession)).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => b.Protein.FullName)).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => string.Join(", ", b.Protein.GeneNames.Select(d => d.Item1 + ":" + d.Item2)))).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => b.Protein.Organism)).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => b.Protein.IsContaminant ? "Y" : "N")).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => b.Protein.IsDecoy ? "Y" : "N")).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => b.PeptideDescription)).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => ("[" + b.OneBasedStartResidueInProtein.ToString(CultureInfo.InvariantCulture) + " to " + b.OneBasedEndResidueInProtein.ToString(CultureInfo.InvariantCulture) + "]"))).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => b.PreviousAminoAcid.ToString())).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => b.NextAminoAcid.ToString())).Item1);
if (FdrInfo != null && FdrInfo.CalculateEValue)
{
int theoreticalsSearched = AllScores[0];
sb.Append('\t' + AllScores[0].ToString());
for (int i = 1; i < AllScores.Count; i++)
{
sb.Append("_" + AllScores[i]);
theoreticalsSearched += AllScores[i];
}
sb.Append('\t' + theoreticalsSearched.ToString());
}
else
{
sb.Append('\t' + " " + '\t' + " ");
}
// Unambiguous
if (IsDecoy)
{
sb.Append("\t" + "D");
}
else if (compactPeptides.Any(b => b.Value.Item2.Any(c => c.Protein.IsContaminant)))
{
sb.Append("\t" + "C");
}
else
{
sb.Append("\t" + "T");
}
}
else
{
sb.Append('\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " ");
}
if (MatchedIonDictOnlyMatches.Any())
{
//Count
sb.Append('\t' + string.Join(";", MatchedIonDictOnlyMatches.Select(b => b.Value.Count(c => c > 0))));
//Masses
sb.Append('\t' + "[");
StringBuilder sbTemp = new StringBuilder();
foreach (var kvp in MatchedIonDictOnlyMatches)
{
sbTemp.Append("[" + string.Join(",", kvp.Value.Select(b => b.ToString("F5", CultureInfo.InvariantCulture))) + "];");
}
sb.Append(GlobalVariables.CheckLengthOfOutput(sbTemp.ToString()));
sb.Append("]");
//Mass error Da
sb.Append('\t' + "[");
sbTemp.Clear();
foreach (var kvp in ProductMassErrorDa)
{
sbTemp.Append("[" + string.Join(",", kvp.Value.Select(b => b.ToString("F5", CultureInfo.InvariantCulture))) + "];");
}
sb.Append(GlobalVariables.CheckLengthOfOutput(sbTemp.ToString()));
sb.Append("]");
//Mass error ppm
sb.Append('\t' + "[");
sbTemp.Clear();
foreach (var kvp in ProductMassErrorPpm)
{
sbTemp.Append("[" + string.Join(",", kvp.Value.Select(b => b.ToString("F2", CultureInfo.InvariantCulture))) + "];");
}
sb.Append(GlobalVariables.CheckLengthOfOutput(sbTemp.ToString()));
sb.Append("]");
}
else
{
sb.Append('\t' + " " + '\t' + " " + '\t' + " " + '\t' + " ");
}
if (LocalizedScores != null)
{
sb.Append('\t' + GlobalVariables.CheckLengthOfOutput(("[" + string.Join(",", LocalizedScores.Select(b => b.ToString("F3", CultureInfo.InvariantCulture))) + "]")));
sb.Append('\t' + (LocalizedScores.Max() - Score).ToString("F3", CultureInfo.InvariantCulture));
}
else
{
sb.Append('\t' + " " + '\t' + " ");
}
if (FdrInfo != null)
{
sb.Append('\t' + FdrInfo.CumulativeTarget.ToString(CultureInfo.InvariantCulture));
sb.Append('\t' + FdrInfo.CumulativeDecoy.ToString(CultureInfo.InvariantCulture));
sb.Append('\t' + FdrInfo.QValue.ToString("F6", CultureInfo.InvariantCulture));
sb.Append('\t' + FdrInfo.CumulativeTargetNotch.ToString(CultureInfo.InvariantCulture));
sb.Append('\t' + FdrInfo.CumulativeDecoyNotch.ToString(CultureInfo.InvariantCulture));
sb.Append('\t' + FdrInfo.QValueNotch.ToString("F6", CultureInfo.InvariantCulture));
if (FdrInfo.CalculateEValue)
{
sb.Append("\t" + FdrInfo.EValue.ToString("F6", CultureInfo.InvariantCulture));
sb.Append("\t" + FdrInfo.EScore.ToString("F6", CultureInfo.InvariantCulture));
}
else
{
sb.Append('\t' + " " + '\t' + " ");
}
}
else
{
sb.Append('\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " ");
}
return(sb.ToString());
}
