/// <summary>
/// Resolve MS-GF+, MSPathFinder, or TopPIC mods with mod definitions
/// </summary>
/// <param name="modList"></param>
/// <param name="peptideMods"></param>
public void ResolveMSGFPlusModsWithModDefinitions(List <ModInfo> modList, PeptideModificationContainer peptideMods)
{
if (modList == null)
{
return;
}
for (var index = 0; index <= modList.Count - 1; index++)
{
var udtModInfo = modList[index];
int resIndexStart;
int resIndexEnd;
if (udtModInfo.Residues.Length > 0)
{
resIndexStart = 0;
resIndexEnd = udtModInfo.Residues.Length - 1;
}
else
{
resIndexStart = -1;
resIndexEnd = -1;
}
for (var residueIndex = resIndexStart; residueIndex <= resIndexEnd; residueIndex++)
{
char chTargetResidue;
if (residueIndex >= 0)
{
chTargetResidue = udtModInfo.Residues[residueIndex];
if (chTargetResidue == '*')
{
// This is a terminal mod, and MSGFDB lists the target residue as * for terminal mods
// This program requires that chTargetResidue be Nothing
chTargetResidue = default;
}
}
else
{
chTargetResidue = default;
}
var modType = ModificationDefinition.ResidueModificationType.DynamicMod;
AminoAcidModInfo.ResidueTerminusState residueTerminusState;
if (udtModInfo.ModType == MSGFPlusModType.DynNTermPeptide)
{
residueTerminusState = AminoAcidModInfo.ResidueTerminusState.PeptideNTerminus;
}
else if (udtModInfo.ModType == MSGFPlusModType.DynCTermPeptide)
{
residueTerminusState = AminoAcidModInfo.ResidueTerminusState.PeptideCTerminus;
}
else if (udtModInfo.ModType == MSGFPlusModType.DynNTermProtein)
{
residueTerminusState = AminoAcidModInfo.ResidueTerminusState.ProteinNTerminus;
}
else if (udtModInfo.ModType == MSGFPlusModType.DynCTermProtein)
{
residueTerminusState = AminoAcidModInfo.ResidueTerminusState.ProteinCTerminus;
}
else
{
switch (chTargetResidue)
{
case AminoAcidModInfo.N_TERMINAL_PEPTIDE_SYMBOL_DMS:
residueTerminusState = AminoAcidModInfo.ResidueTerminusState.PeptideNTerminus;
if (udtModInfo.ModType == MSGFPlusModType.StaticMod)
{
modType = ModificationDefinition.ResidueModificationType.TerminalPeptideStaticMod;
}
break;
case AminoAcidModInfo.C_TERMINAL_PEPTIDE_SYMBOL_DMS:
residueTerminusState = AminoAcidModInfo.ResidueTerminusState.PeptideCTerminus;
if (udtModInfo.ModType == MSGFPlusModType.StaticMod)
{
modType = ModificationDefinition.ResidueModificationType.TerminalPeptideStaticMod;
}
break;
case AminoAcidModInfo.N_TERMINAL_PROTEIN_SYMBOL_DMS:
residueTerminusState = AminoAcidModInfo.ResidueTerminusState.ProteinNTerminus;
if (udtModInfo.ModType == MSGFPlusModType.StaticMod)
{
modType = ModificationDefinition.ResidueModificationType.ProteinTerminusStaticMod;
}
break;
case AminoAcidModInfo.C_TERMINAL_PROTEIN_SYMBOL_DMS:
residueTerminusState = AminoAcidModInfo.ResidueTerminusState.ProteinCTerminus;
if (udtModInfo.ModType == MSGFPlusModType.StaticMod)
{
modType = ModificationDefinition.ResidueModificationType.ProteinTerminusStaticMod;
}
break;
default:
residueTerminusState = AminoAcidModInfo.ResidueTerminusState.None;
if (udtModInfo.ModType == MSGFPlusModType.StaticMod)
{
modType = ModificationDefinition.ResidueModificationType.StaticMod;
}
break;
}
}
var modificationDefinition = peptideMods.LookupModificationDefinitionByMassAndModType(
udtModInfo.ModMassVal, modType, chTargetResidue, residueTerminusState, out _, true);
if (residueIndex == resIndexStart)
{
// Update the Mod Symbol
udtModInfo.ModSymbol = modificationDefinition.ModificationSymbol;
}
}
modList[index] = udtModInfo;
}
}
/// <summary>
/// Constructor
/// </summary>
/// <remarks>
/// The base class constructor calls InitializeLocalVariables,
/// which calls both the base class's Clear method and this class's Clear method
/// </remarks>
/// <param name="peptideMods"></param>
/// <param name="peptideSeqMassCalculator"></param>
public MODaResults(PeptideModificationContainer peptideMods, PeptideMassCalculator peptideSeqMassCalculator)
: base(peptideMods, peptideSeqMassCalculator)
{
}
