public static SpectrumPeakAnnotation Create(SmallMoleculeLibraryAttributes mol, Adduct adduct, string comment, double?mzTheoretical)
{
double?massTheoretical = mzTheoretical.HasValue ? adduct.MassFromMz(mzTheoretical.Value, MassType.Monoisotopic).Value : (double?)null;
var ion = new CustomIon(mol, adduct, massTheoretical);
if ((mzTheoretical ?? 0.0) > 0)
{
if (Equals(ion.MonoisotopicMassMz, 0.0))
{
// We didn't have enough info to calculate mz, use the provided theoretical value
var massMono = adduct.MassFromMz(mzTheoretical.Value, MassType.Monoisotopic);
var massAverage = adduct.MassFromMz(mzTheoretical.Value, MassType.Average);
ion = new CustomIon(ion.GetSmallMoleculeLibraryAttributes(), ion.Adduct, massMono, massAverage);
}
else
{
// Check our calculated value against provided theoretical value, allowing quite a lot of wiggle (not everybody is using the same precision out there)
var delta = .5; // Generous error for sanity check
if (Math.Abs(ion.MonoisotopicMassMz - mzTheoretical.Value) > delta)
{
Assume.Fail(string.Format(@"SpectrumPeakAnnotation: mzTheoretical {0} and mzActual {1} disagree by more than {2} in {3} {4}",
mzTheoretical, ion.MonoisotopicMassMz, delta, ion, comment ?? string.Empty));
}
}
}
return(ion.IsEmpty && string.IsNullOrEmpty(comment) ?
EMPTY :
new SpectrumPeakAnnotation(ion, comment));
}
// Cannot find a way to use anything but a file with SQLite
// public const string _bibliospecLiteLibPath = @"C:\Libraries\yeast.blib";
private List <SpectrumPeakAnnotation> MakeTestPeakAnnotation(Adduct adduct, float mz, string name, string note)
{
var ion = new CustomIon(null, adduct,
adduct.MassFromMz(mz, MassType.Monoisotopic),
adduct.MassFromMz(mz, MassType.Average),
name);
var annot = SpectrumPeakAnnotation.Create(ion, note);
return(new List <SpectrumPeakAnnotation> {
annot
});
}
/// <summary>
/// Get a mass value from the text string, treating the string as m/z info if we have a charge state
/// </summary>
private double?GetMassFromText(string text, MassType massType)
{
try
{
if (String.IsNullOrEmpty(text))
{
return(null);
}
else
{
double parsed = double.Parse(text);
if (!Adduct.IsEmpty)
{
// Convert from m/z to mass
return(Adduct.MassFromMz(parsed, massType));
}
return(parsed);
}
}
catch (Exception)
{
return(null);
}
}