/// <summary>
/// Create a spectrum identification item for the mzid; scores, peptide, and peptideEvidences must be added. Calculated m/z can also be added.
/// </summary>
/// <param name="spectraSource">source object for the spectrum, returned from <see cref="AddSpectraData"/></param>
/// <param name="nativeId">native id of the spectrum</param>
/// <param name="retentionTimeMinutes">retention time in minutes of the spectrum</param>
/// <param name="expMz">experimental m/z of the peptide</param>
/// <param name="charge">Charge of the peptide</param>
/// <param name="rank">rank of result for a spectrum; may be the same as another result for the same spectrum if they score equally</param>
/// <param name="calcMz">(optional) Calculated m/z of the peptide; default double.NaN (not added)</param>
/// <returns>Object: Must populate PeptideEvidences and Peptide, as well as add score information to CVParams and UserParams</returns>
public SpectrumIdentificationItemObj AddSpectrumIdentification(SpectraDataObj spectraSource, string nativeId, double retentionTimeMinutes, double expMz, int charge, int rank = 1, double calcMz = double.NaN)
{
SpectrumIdentificationResultObj specResult;
if (!identificationResults.TryGetValue(nativeId, out specResult))
{
specResult = new SpectrumIdentificationResultObj()
{
SpectrumID = nativeId,
SpectraData = spectraSource,
SpectrumIdentificationItems = new IdentDataList <SpectrumIdentificationItemObj>(),
CVParams = new IdentDataList <CVParamObj>(),
UserParams = new IdentDataList <UserParamObj>(),
};
identificationResults.Add(nativeId, specResult);
var number = nativeId.Split('=').Last();
specResult.Id = "SIR_" + number;
var rt = new CVParamObj(CV.CV.CVID.MS_scan_start_time, retentionTimeMinutes.ToString(CultureInfo.InvariantCulture))
{
UnitCvid = CV.CV.CVID.UO_minute,
};
specResult.CVParams.Add(rt);
}
var specIdent = new SpectrumIdentificationItemObj()
{
Id = specResult.Id + "_" + (specResult.SpectrumIdentificationItems.Count + 1),
PeptideEvidences = new IdentDataList <PeptideEvidenceRefObj>(),
ChargeState = charge,
ExperimentalMassToCharge = expMz,
Rank = rank,
PassThreshold = true,
CVParams = new IdentDataList <CVParamObj>(),
UserParams = new IdentDataList <UserParamObj>(),
};
if (!calcMz.Equals(double.NaN))
{
specIdent.CalculatedMassToCharge = calcMz;
}
specResult.SpectrumIdentificationItems.Add(specIdent);
return(specIdent);
}
public SpectrumIdentificationItemWrapper(SpectrumIdentificationResultObj specResult, SpectrumIdentificationItemObj specIdent)
{
SpectrumResult = specResult;
SpectrumIdentification = specIdent;
}
