public static CometParams FileContentsToCometParams(string fileContents)
{
var config = CometParams.GetIonTrapParams();
var fileLines = fileContents.Split(Environment.NewLine.ToCharArray(), StringSplitOptions.RemoveEmptyEntries);
var rx = new Regex(@"^([\w]+)\s*=\s*([\w\s\.]+)");
foreach (var nextLine in fileLines)
{
if (!rx.IsMatch(nextLine))
{
continue;
}
var match = rx.Match(nextLine);
if (match.Groups.Count < 3)
{
continue;
}
double nextNumber;
var validNumber = double.TryParse(match.Groups[2].Value, out nextNumber);
switch (match.Groups[1].Value)
{
case "peptide_mass_tolerance":
if (!validNumber)
{
break;
}
config.PrecursorTolerance = nextNumber;
break;
case "peptide_mass_units":
if (!validNumber)
{
break;
}
config.PrecursorUnit = (int)nextNumber;
break;
case "search_enzyme_number":
if (!validNumber)
{
break;
}
config.CleavageAgent = (int)nextNumber;
break;
case "num_enzyme_termini":
if (!validNumber)
{
break;
}
config.Specificity = (int)nextNumber;
break;
case "allowed_missed_cleavage":
if (!validNumber)
{
break;
}
config.MaxMissedCleavages = (int)nextNumber;
break;
case "max_variable_mods_in_peptide":
if (!validNumber)
{
break;
}
config.MaxMods = (int)nextNumber;
break;
case "fragment_bin_tol":
if (!validNumber)
{
break;
}
config.FragmentBinTolerance = nextNumber;
break;
case "fragment_bin_offset":
if (!validNumber)
{
break;
}
config.FragmentBinOffset = nextNumber;
break;
case "add_C_cysteine":
if (!validNumber)
{
break;
}
config.StaticCysteineMod = nextNumber;
break;
}
if (match.Groups[1].Value.StartsWith("variable_mod"))
{
var splitValue = match.Groups[2].Value.Split(" ".ToCharArray(),
StringSplitOptions.RemoveEmptyEntries);
if (splitValue.Length < 4)
{
continue;
}
double massShift;
if (!double.TryParse(splitValue[0], out massShift))
{
continue;
}
config.DynamicModifications.Add(new CometParams.Modification(splitValue[1], massShift));
}
}
return(config);
}
