/// <summary>
/// Get the number of proteoform sequences possible with the provided number of dynamic modifications
/// </summary>
/// <param name="nDynMods"></param>
/// <returns></returns>
public double GetNumProteoformSequencesByNumMods(int nDynMods)
{
if (nDynMods < 1 || nDynMods > ModificationParams.MaxNumDynModsPerSequence)
{
return(0);
}
var numModCombs = _graph[_index].Length;
var nProteoforms = 0d;
for (var modIndex = 0; modIndex < numModCombs; modIndex++)
{
var modCombs = ModificationParams.GetModificationCombination(_graph[_index][modIndex].ModificationCombinationIndex);
if (modCombs.GetNumModifications() < nDynMods)
{
continue;
}
if (modCombs.GetNumModifications() > nDynMods)
{
break;
}
nProteoforms += GetNumProteoformSequences(modIndex);
//if (nProteoforms > double.MaxValue) return double.MaxValue; // overflow
}
return(nProteoforms);
}
/// <summary>
/// Get the modification combinations in the current sequence graph
/// </summary>
/// <returns></returns>
public ModificationCombination[] GetModificationCombinations()
{
var numModCombs = _graph[_index].Length;
var modCombs = new ModificationCombination[numModCombs];
for (var modIndex = 0; modIndex < numModCombs; modIndex++)
{
modCombs[modIndex] = ModificationParams.GetModificationCombination(_graph[_index][modIndex].ModificationCombinationIndex);
}
return(modCombs);
}
public void TestModificationParams()
{
var methodName = MethodBase.GetCurrentMethod().Name;
ShowStarting(methodName);
var modifications = new[] { Modification.Acetylation, Modification.Phosphorylation, Modification.Oxidation}; //, Modification.PyroGluQ };
var modParams = new ModificationParams(modifications, 3);
int numCombinations = modParams.NumModificationCombinations;
for (int modCombIndex = 0; modCombIndex < numCombinations; modCombIndex++)
{
var modCombination = modParams.GetModificationCombination(modCombIndex);
Console.WriteLine("{0}: {1} {2} {3}", modCombIndex, modCombination, modCombination.Composition, modCombination.Composition.Mass);
}
Console.WriteLine(modParams.GetModificationCombinationIndex(8, 0));
Console.WriteLine(modParams.GetModificationCombinationIndex(19, 1));
}
