public MzidResultsWriter(FastaDatabase db, LcMsRun run, MsPfParameters options)
{
this.database = db;
this.lcmsRun = run;
this.options = options;
}
/// <summary>
/// Opens parameter file from .PARAM file..
/// </summary>
/// <param name="filePath">The path of the parameter file.</param>
/// <returns>
/// Parsed MSPathFinder parameters. Returns null if file does not exist.
/// Throws exception if file is not formatted correctly.
/// </returns>
public static MsPfParameters Parse(string filePath)
{
if (!File.Exists(filePath))
{
return(null);
}
var file = File.ReadAllLines(filePath);
var param = new MsPfParameters();
foreach (var line in file)
{
var parts = line.Split('\t');
if (parts.Length < 2)
{
continue;
}
switch (parts[0])
{
case "SpecFile":
param.SpecFilePath = parts[1];
break;
case "DatabaseFile":
param.DatabaseFilePath = parts[1];
break;
case "FeatureFile":
param.FeatureFilePath = parts[1];
break;
case "SearchMode":
#pragma warning disable 618
param.SearchModeInt = Convert.ToInt32(parts[1]);
#pragma warning restore 618
break;
case "InternalCleavageMode":
param.InternalCleavageMode = (InternalCleavageType)Enum.Parse(typeof(InternalCleavageType), parts[1]);
break;
case "Tda":
int tda = 0;
tda += Convert.ToInt32(parts[1].Contains("Target"));
tda += Convert.ToInt32(parts[1].Contains("Decoy")) * 2;
param.TargetDecoySearchMode = (DatabaseSearchMode)tda;
break;
case "PrecursorIonTolerancePpm":
param.PrecursorIonTolerance = new Tolerance(Convert.ToDouble(parts[1]), ToleranceUnit.Ppm);
break;
case "ProductIonTolerancePpm":
param.ProductIonTolerance = new Tolerance(Convert.ToDouble(parts[1]), ToleranceUnit.Ppm);
break;
case "MinSequenceLength":
param.MinSequenceLength = Convert.ToInt32(parts[1]);
break;
case "MaxSequenceLength":
param.MaxSequenceLength = Convert.ToInt32(parts[1]);
break;
case "MinPrecursorIonCharge":
param.MinPrecursorIonCharge = Convert.ToInt32(parts[1]);
break;
case "MaxPrecursorIonCharge":
param.MaxPrecursorIonCharge = Convert.ToInt32(parts[1]);
break;
case "MinProductIonCharge":
param.MinProductIonCharge = Convert.ToInt32(parts[1]);
break;
case "MaxProductIonCharge":
param.MaxProductIonCharge = Convert.ToInt32(parts[1]);
break;
case "MinSequenceMass":
param.MinSequenceMass = Convert.ToDouble(parts[1]);
break;
case "MaxSequenceMass":
param.MaxSequenceMass = Convert.ToDouble(parts[1]);
break;
case "MinFeatureProbability":
param.MinFeatureProbablility = Convert.ToDouble(parts[1]);
break;
case "MaxDynamicModificationsPerSequence":
param.MaxDynamicModificationsPerSequence = Convert.ToInt32(parts[1]);
break;
case "Modification":
param.Modifications.AddRange(ModFileParser.ParseModification(parts[1]));
break;
case "ActivationMethod":
param.ActivationMethod = (ActivationMethod)Convert.ToInt32(parts[1]);
break;
}
}
if (param.PrecursorIonTolerance == null && param.ProductIonTolerance != null)
{
param.PrecursorIonTolerance = param.ProductIonTolerance;
}
if (param.PrecursorIonTolerance != null && param.ProductIonTolerance == null)
{
param.ProductIonTolerance = param.PrecursorIonTolerance;
}
return(param);
}
