public static string MSGFParamsToOverload(MSGFParams config)
{
return("-inst " + config.Instrument
+ " -o \"[FileNameOnly]" + config.OutputSuffix + ".mzid\""
+ " -tda 1"
+ " -m 0"// + config.FragmentationMethod
+ " -protocol " + config.Protocol
+ " -e " + config.CleavageAgent
+ " -t " + config.PrecursorTolerance.ToString(CultureInfo.InvariantCulture) + config.PrecursorToleranceUnits
+ " -ti " + config.IsotopeErrorMin + "," + config.IsotopeErrorMax
+ " -ntt " + config.Specificity
+ " -s \"[FullFileName]\"");
}
public static MSGFParams OverloadToMSGFParams(string overloadString)
{
var config = new MSGFParams();
var splitOverload = overloadString.Split();
for (var x = 0; x < splitOverload.Length; x++)
{
var nextNumber = -999;
var validNumberNext = false;
if (x + 1 < splitOverload.Length)
{
validNumberNext = int.TryParse(splitOverload[x + 1], out nextNumber);
}
switch (splitOverload[x])
{
case "-inst":
if (validNumberNext)
{
config.Instrument = nextNumber;
}
break;
case "-o":
var trimmedString = splitOverload[x + 1].Replace("\"[FileNameOnly]", string.Empty)
.Replace(".mzid\"", string.Empty);
config.OutputSuffix = trimmedString;
break;
//case "-m":
// if (validNumberNext)
// config.FragmentationMethod = nextNumber;
break;
case "-e":
if (validNumberNext)
{
config.CleavageAgent = nextNumber;
}
break;
case "-p":
if (validNumberNext)
{
config.Protocol = nextNumber;
}
break;
case "-t":
if (x + 1 < splitOverload.Length)
{
double tolerance;
var rx = new Regex(@"([\.\d]+)([A-Za-z]+)");
if (!rx.IsMatch(splitOverload[x + 1]))
{
break;
}
var groups = rx.Match(splitOverload[x + 1]).Groups;
if (groups.Count != 3 || !double.TryParse(groups[1].Value, out tolerance))
{
break;
}
config.PrecursorTolerance = tolerance;
config.PrecursorToleranceUnits = groups[2].Value;
}
break;
case "-ti":
if (x + 1 < splitOverload.Length)
{
int min;
int max;
var splitNext = splitOverload[x + 1].Split(',');
if (splitNext.Length != 2)
{
break;
}
if (!int.TryParse(splitNext[0], out min) || !int.TryParse(splitNext[1], out max))
{
break;
}
config.IsotopeErrorMin = min;
config.IsotopeErrorMax = max;
}
break;
case "-ntt":
if (validNumberNext)
{
config.Specificity = nextNumber;
}
break;
}
}
return(config);
}
public static MSGFParams OverloadToMSGFParams(string overloadString)
{
var config = new MSGFParams();
var splitOverload = overloadString.Split();
for (var x = 0; x < splitOverload.Length; x++)
{
var nextNumber=-999;
var validNumberNext = false;
if (x + 1 < splitOverload.Length)
validNumberNext = int.TryParse(splitOverload[x + 1], out nextNumber);
switch (splitOverload[x])
{
case "-inst":
if (validNumberNext)
config.Instrument = nextNumber;
break;
case "-o":
var trimmedString = splitOverload[x + 1].Replace("\"[FileNameOnly]", string.Empty)
.Replace(".mzid\"", string.Empty);
config.OutputSuffix = trimmedString;
break;
//case "-m":
// if (validNumberNext)
// config.FragmentationMethod = nextNumber;
break;
case "-e":
if (validNumberNext)
config.CleavageAgent = nextNumber;
break;
case "-p":
if (validNumberNext)
config.Protocol = nextNumber;
break;
case "-t":
if (x + 1 < splitOverload.Length)
{
double tolerance;
var rx = new Regex(@"([\.\d]+)([A-Za-z]+)");
if (!rx.IsMatch(splitOverload[x + 1]))
break;
var groups = rx.Match(splitOverload[x + 1]).Groups;
if (groups.Count != 3 || !double.TryParse(groups[1].Value, out tolerance))
break;
config.PrecursorTolerance = tolerance;
config.PrecursorToleranceUnits = groups[2].Value;
}
break;
case "-ti":
if (x + 1 < splitOverload.Length)
{
int min;
int max;
var splitNext = splitOverload[x + 1].Split(',');
if (splitNext.Length != 2)
break;
if (!int.TryParse(splitNext[0], out min) || !int.TryParse(splitNext[1], out max))
break;
config.IsotopeErrorMin = min;
config.IsotopeErrorMax = max;
}
break;
case "-ntt":
if (validNumberNext)
config.Specificity = nextNumber;
break;
}
}
return config;
}
public static string MSGFParamsToOverload(MSGFParams config)
{
return "-inst " + config.Instrument
+ " -o \"[FileNameOnly]" + config.OutputSuffix + ".mzid\""
+ " -tda 1"
+ " -m 0"// + config.FragmentationMethod
+ " -protocol " + config.Protocol
+ " -e " + config.CleavageAgent
+ " -t " + config.PrecursorTolerance.ToString(CultureInfo.InvariantCulture) + config.PrecursorToleranceUnits
+ " -ti " + config.IsotopeErrorMin + "," + config.IsotopeErrorMax
+ " -ntt " + config.Specificity
+ " -s \"[FullFileName]\"";
}