/// <summary>
/// Check that an AA from the list of modifications is found in the XML modification.
/// </summary>
private static bool ContainsSite(mod_t modification, string aa, out List <string> losses)
{
losses = new List <string>();
foreach (specificity_t specificty in modification.specificity)
{
if (Equals(specificty.site, aa) ||
(aa.Length > 1 && specificty.position.ToString().ToLower().Contains(aa.ToLower().Replace("-", ""))))
{
if (specificty.NeutralLoss != null && specificty.NeutralLoss.Length > 0)
{
foreach (NeutralLoss_t loss in specificty.NeutralLoss)
{
// ReSharper disable CompareOfFloatsByEqualityOperator
if (loss.avge_mass == 0)
{
// ReSharper restore CompareOfFloatsByEqualityOperator
continue;
}
losses.Add(BuildFormula(loss.element));
}
}
losses.Sort();
return(true);
}
}
return(false);
}
/// <summary>
/// Check for label atoms in the given sequence matching the given aa, and create a corresponding string if found.
/// </summary>
private static bool CheckLabelAtoms(mod_t mod, char[] aas, out string labelAtomsFormula)
{
labelAtomsFormula = "";
bool hasLabelAtoms = true;
if (mod.title.StartsWith("Label"))
{
foreach (var element in mod.delta.element)
{
char elementMatch;
if (hasLabelAtoms && DICT_HEAVY_LABELS.TryGetValue(element.symbol, out elementMatch))
{
foreach (char aa in aas)
{
int numInFormula = ParseSeqMassCalcFormula(aa, elementMatch);
if (!Equals(element.number, numInFormula.ToString(CultureInfo.InvariantCulture)))
{
hasLabelAtoms = false;
break;
}
}
if (!string.IsNullOrEmpty(labelAtomsFormula))
{
labelAtomsFormula += '|';
}
var symbol = element.symbol;
var elementIndex = symbol.IndexOfAny(new[] { 'N', 'C', 'O', 'H' });
labelAtomsFormula += "LabelAtoms." + symbol[elementIndex] + symbol.Remove(elementIndex);
}
else if (element.symbol.Length == 1 && DICT_HEAVY_LABELS.ContainsValue(element.symbol[0]))
{
foreach (char aa in aas)
{
int numInFormula = ParseSeqMassCalcFormula(aa, element.symbol[0]);
if ((Int32.Parse(element.number) * -1) > numInFormula)
{
return(false);
}
}
}
}
}
if (!hasLabelAtoms || string.IsNullOrEmpty(labelAtomsFormula))
{
labelAtomsFormula = "LabelAtoms.None";
}
return(true);
}
/// <summary>
/// Check that an AA from the list of modifications is found in the XML modification.
/// </summary>
private static bool ContainsSite(mod_t modification, string aa, out List<string> losses)
{
losses = new List<string>();
foreach (specificity_t specificty in modification.specificity)
{
if (Equals(specificty.site, aa) ||
(aa.Length > 1 && specificty.position.ToString().ToLower().Contains(aa.ToLower().Replace("-", ""))))
{
if (specificty.NeutralLoss != null && specificty.NeutralLoss.Length > 0)
{
foreach(NeutralLoss_t loss in specificty.NeutralLoss)
{
// ReSharper disable CompareOfFloatsByEqualityOperator
if(loss.avge_mass == 0)
// ReSharper restore CompareOfFloatsByEqualityOperator
continue;
losses.Add(BuildFormula(loss.element));
}
}
losses.Sort();
return true;
}
}
return false;
}
/// <summary>
/// Check for label atoms in the given sequence matching the given aa, and create a corresponding string if found.
/// </summary>
private static bool CheckLabelAtoms(mod_t mod, char[] aas, out string labelAtomsFormula)
{
labelAtomsFormula = "";
bool hasLabelAtoms = true;
if (mod.title.StartsWith("Label"))
{
foreach (var element in mod.delta.element)
{
char elementMatch;
if (hasLabelAtoms && DICT_HEAVY_LABELS.TryGetValue(element.symbol, out elementMatch))
{
foreach (char aa in aas)
{
int numInFormula = ParseSeqMassCalcFormula(aa, elementMatch);
if (!Equals(element.number, numInFormula.ToString(CultureInfo.InvariantCulture)))
{
hasLabelAtoms = false;
break;
}
}
if (!string.IsNullOrEmpty(labelAtomsFormula))
labelAtomsFormula += '|';
var symbol = element.symbol;
var elementIndex = symbol.IndexOfAny(new[] { 'N', 'C', 'O', 'H' });
labelAtomsFormula += "LabelAtoms." + symbol[elementIndex] + symbol.Remove(elementIndex);
}
else if (element.symbol.Length == 1 && DICT_HEAVY_LABELS.ContainsValue(element.symbol[0]))
{
foreach (char aa in aas)
{
int numInFormula = ParseSeqMassCalcFormula(aa, element.symbol[0]);
if ((Int32.Parse(element.number) * -1) > numInFormula)
return false;
}
}
}
}
if (!hasLabelAtoms || string.IsNullOrEmpty(labelAtomsFormula))
labelAtomsFormula = "LabelAtoms.None";
return true;
}
