/// <summary>
/// Generates a theoretical spectra based on a modification list and positions for those modifications
/// </summary>
/// <param name="positions">int array has modifications at indice in which they occur in the sequence</param>
/// <param name="myMods">dynamic modification list</param>
/// <returns>Dictionary of theoretical ions organized by charge</returns>
public Dictionary <int, ChargeStateIons> GetTempSpectra(int[] positions, List <DynamicModification> myMods)
{
Dictionary <int, ChargeStateIons> tempFragIons = new Dictionary <int, ChargeStateIons>();
for (int i = 1; i < chargeState; ++i)
{
tempFragIons[i] = ChargeStateIons.GenerateFragmentIon(i, MassType.Monoisotopic,
myMods, positions,
bIonsMonoisotopicMass, yIonsMonoisotopicMass, fht.Length);
}
return(tempFragIons);
}
/// <summary>
/// Creates a new fragment ion based on the given parameters.
/// </summary>
/// <param name="chargeState">Desired charge state for the fragment ion.
/// Must be greater than 0.</param>
/// <param name="massType">Mass type.</param>
/// <param name="minPhosphoSite">The smallest from the list of available
/// phophoSites for this peptide.</param>
/// <param name="maxPhosphoSite">The biggest from the list of available
/// phophoSites for this peptide.</param>
/// <param name="bIons">The bIons to use corresponding to the mass type.</param>
/// <param name="yIons">The yIons to use corresponding to the mass type.</param>
/// <param name="peptideLength">The length of the trimmed peptide without
/// phosphorylation sites.</param>
/// <returns>A newly constructed FragmentIon upon success, null if any
/// errors occured during construction.</returns>
public static ChargeStateIons GenerateFragmentIon(int chargeState,
MassType massType, List <Mod.DynamicModification> dynamMods, int[] positions,
List <double> bIons, List <double> yIons, int peptideLength)
{
ChargeStateIons fragIon = null;
MolecularWeights.MassType = massType;
double sumofModsB = 0.0;
double sumofModsY = 0.0;
// If the charge state is one, create the
if (chargeState == 1)
{
fragIon = new ChargeStateIons();
// Set the charge state of the frag ion
fragIon.chargeState = chargeState;
// There is a phosphorylation site
if (dynamMods.Count > 0)
{
// bIons
for (int i = 0; i < bIons.Count; ++i)
{
foreach (Mod.DynamicModification mod in dynamMods)
{
if (mod.UniqueID == positions[i])
{
sumofModsB += mod.MassMonoisotopic;
}
if (mod.UniqueID == positions[peptideLength - 1 - i])
{
sumofModsY += mod.MassMonoisotopic;
}
}
fragIon.bIonsOut.Add(bIons[i] + sumofModsB);
fragIon.yIonsOut.Add(yIons[i] + sumofModsY);
}
}
}
else if (chargeState > 1)
{
sumofModsB = (chargeState - 1) * MolecularWeights.Hydrogen;;
sumofModsY = sumofModsB;
fragIon = new ChargeStateIons();
// Set the charge state of the frag ion
fragIon.chargeState = chargeState;
// The value to add to each ion
double temp = (chargeState - 1) * MolecularWeights.Hydrogen;
// There is a phosphorylation site
if (dynamMods.Count > 0)
{
for (int i = 0; i < bIons.Count; ++i)
{
foreach (Mod.DynamicModification mod in dynamMods)
{
if (mod.UniqueID == positions[i])
{
sumofModsB += mod.MassMonoisotopic;
}
if (mod.UniqueID == positions[peptideLength - 1 - i])
{
sumofModsY += mod.MassMonoisotopic;
}
}
fragIon.bIonsOut.Add((bIons[i] + sumofModsB) / chargeState);
fragIon.yIonsOut.Add((yIons[i] + sumofModsY) / chargeState);
}
}
}
return(fragIon);
}