/// <summary>
/// Handle a single SpectrumIdentificationResult element and child nodes
/// Called by ReadSpectrumIdentificationList (xml hierarchy)
/// </summary>
/// <param name="result">PSM result</param>
/// <param name="psmResults"></param>
private void ProcessSpectrumIdentificationResult(SimpleMZIdentMLReader.SpectrumIdItem result, ICollection <IdentData> psmResults)
{
var data = new IdentData
{
NativeId = result.NativeId,
ScanId = (ulong)result.ScanNum,
ScanTimeSeconds = result.ScanTimeMinutes * 60,
CalcMz = result.CalMz,
ExperMz = result.ExperimentalMz,
Charge = result.Charge,
ThresholdValue = result.SpecEv // MS-GF:SpecEValue
};
//data.MassError = data.ExperMz - data.CalcMz;
//data.PpmError = (data.MassError / data.CalcMz) * 1.0e6;
if (IdentProg == IdentProgramType.MyriMatch &&
result.AllParamsDict.TryGetValue("MyriMatch:MVH", out var valueText) &&
double.TryParse(valueText, out var value))
{
data.ThresholdValue = value;
}
if (PassesThreshold(data) && PassesWindows(data))
{
psmResults.Add(data);
}
if (data.ScanTimeSeconds > 0)
{
HaveScanTimes = true;
}
}
/// <summary>
/// Read results from tsv file into group of objects from PSI_Interface
/// </summary>
/// <param name="idFilePath"></param>
/// <returns></returns>
public static SimpleMZIdentMLReader.SimpleMZIdentMLData ReadResultsFromFileToMzIdData(string idFilePath)
{
var databaseSearchResultData = ReadResultsFromFile(idFilePath);
var simpleMzIdentMLData = new SimpleMZIdentMLReader.SimpleMZIdentMLData(idFilePath);
foreach (var databaseSearchResult in databaseSearchResultData)
{
var peptide = new SimpleMZIdentMLReader.PeptideRef
{
Sequence = databaseSearchResult.Sequence
};
var identification = new SimpleMZIdentMLReader.SpectrumIdItem
{
Peptide = peptide,
Charge = databaseSearchResult.Charge,
ScanNum = databaseSearchResult.ScanNum,
SpecEv = databaseSearchResult.SpecEValue,
};
// Parse modification
var modParts = databaseSearchResult.Modifications.Split(',');
if (modParts.Length > 0)
{
foreach (var part in modParts)
{
var mod = part.Split(' ');
if (mod.Length < 2)
{
continue;
}
var modName = mod[0];
var modIndex = Convert.ToInt32(mod[1]);
var ipMod = Modification.Get(modName);
var modification = new SimpleMZIdentMLReader.Modification
{
Mass = ipMod.Mass,
Tag = modName,
};
peptide.ModsAdd(modIndex, modification);
}
}
var proteinAccessions = databaseSearchResult.ProteinName.Split(',');
foreach (var accession in proteinAccessions)
{
var dbSequence = new SimpleMZIdentMLReader.DatabaseSequence
{
Accession = accession.Trim(),
ProteinDescription = databaseSearchResult.ProteinDescription
};
var peptideEvidence = new SimpleMZIdentMLReader.PeptideEvidence
{
DbSeq = dbSequence,
Pre = databaseSearchResult.Pre,
Post = databaseSearchResult.Post,
PeptideRef = identification.Peptide,
Start = databaseSearchResult.Start,
End = databaseSearchResult.End,
};
identification.PepEvidence.Add(peptideEvidence);
}
simpleMzIdentMLData.Identifications.Add(identification);
}
return(simpleMzIdentMLData);
}
