public IFragmentMassCalc GetFragmentCalc(IsotopeLabelType labelType, ExplicitMods mods)
{
var massCalcBase = GetBaseCalc(labelType, mods, _fragmentMassCalcs);
if (massCalcBase != null)
{
// If this type is not explicitly modified, then it must be
// heavy with explicit light modifications.
if (!mods.IsModified(labelType))
labelType = IsotopeLabelType.light;
if (!labelType.IsLight && !mods.HasModifications(labelType))
return null;
return new ExplicitSequenceMassCalc(mods, massCalcBase, labelType);
}
return GetMassCalc(labelType, _fragmentMassCalcs);
}
public RelativeRT GetRelativeRT(IsotopeLabelType labelType, string seq, ExplicitMods mods)
{
if (labelType.IsLight)
return RelativeRT.Matching;
// Default is matching
RelativeRT relativeRT = RelativeRT.Matching;
// One unkown modification makes everything unknown
// One preceding modification with no unknowns make relative RT preceding
// Overlapping overrides matching
if (mods != null && mods.IsModified(labelType))
{
foreach (var mod in mods.GetModifications(labelType))
{
if (mod.Modification.RelativeRT == RelativeRT.Unknown)
return RelativeRT.Unknown;
if (mod.Modification.RelativeRT == RelativeRT.Preceding)
relativeRT = RelativeRT.Preceding;
else if (mod.Modification.RelativeRT == RelativeRT.Overlapping &&
relativeRT == RelativeRT.Matching)
relativeRT = RelativeRT.Overlapping;
}
}
else
{
foreach (var mod in PeptideSettings.Modifications.GetModifications(labelType))
{
if (!mod.IsMod(seq))
continue;
if (mod.RelativeRT == RelativeRT.Unknown)
return RelativeRT.Unknown;
if (mod.RelativeRT == RelativeRT.Preceding)
relativeRT = RelativeRT.Preceding;
else if (mod.RelativeRT == RelativeRT.Overlapping &&
relativeRT == RelativeRT.Matching)
relativeRT = RelativeRT.Overlapping;
}
}
return relativeRT;
}
private static SequenceMassCalc GetBaseCalc(IsotopeLabelType labelType,
ExplicitMods mods, IList<TypedMassCalc> massCalcs)
{
if (mods == null)
return null;
var calcLightImplicit = massCalcs[0].MassCalc;
// If the light type is not modified
if (!mods.IsModified(IsotopeLabelType.light))
{
// If requesting the light calculator or an unmodified heavy,
// then no explicit calculator is required.
if (labelType.IsLight || !mods.IsModified(labelType))
return null;
// Otherwise, use its calculator as the base for a heavy type
// to make sure the implicit light modifications are included.
return calcLightImplicit;
}
// If the type requested is not modified, it must be a heavy type
// with the light type modified. In this case, return the heavy
// calculator as the base, to which the light explicit modifications
// may be applied to get modified masses.
if (!mods.IsModified(labelType))
return GetMassCalc(labelType, massCalcs);
// If the light modifications are variable, and this is a type for
// which explicit modifications exist (including the light type itself),
// then return the light calculator as base.
if (mods.IsVariableStaticMods)
return calcLightImplicit;
// If both light and this type are modified, then us a base calculator
// that contains no modifications at all.
return (calcLightImplicit.MassType == MassType.Monoisotopic ?
MonoisotopicMassCalc : AverageMassCalc);
}
