/// <summary>
/// Initializes a new instance of the <see cref="SearchSettingsViewModel"/> class.
/// Initializes from <see cref="Models.MsPfParameters" />, MSPathFinder parameters.
/// </summary>
/// <param name="dialogService">Dialog service for opening dialogs from view model</param>
/// <param name="mspfParameters">The MSPathFinder parameters.</param>
public SearchSettingsViewModel(IMainDialogService dialogService, MsPfParameters mspfParameters) : this(dialogService)
{
if (mspfParameters == null)
{
return;
}
SearchModifications.AddRange(
mspfParameters.Modifications.Select(
searchMod => new SearchModificationViewModel(this.dialogService)
{
SearchModification = searchMod
}));
MinSequenceLength = mspfParameters.MinSequenceLength;
MaxSequenceLength = mspfParameters.MaxSequenceLength;
MinSequenceMass = mspfParameters.MinSequenceMass;
MaxSequenceMass = mspfParameters.MaxSequenceMass;
MinPrecursorIonCharge = mspfParameters.MinPrecursorIonCharge;
MaxPrecursorIonCharge = mspfParameters.MaxPrecursorIonCharge;
MinProductIonCharge = mspfParameters.MinProductIonCharge;
MaxProductIonCharge = mspfParameters.MaxPrecursorIonCharge;
PrecursorIonToleranceValue = mspfParameters.PrecursorTolerancePpm.GetValue();
ProductIonToleranceValue = mspfParameters.ProductIonTolerancePpm.GetValue();
MaxDynamicModificationsPerSequence =
mspfParameters.MaxDynamicModificationsPerSequence;
}
/// <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>
private static MsPfParameters ReadFromParameterFile(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.PuSpecFile = parts[1];
break;
case "DatabaseFile":
param.DatabaseFile = parts[1];
break;
case "FeatureFile":
param.FeatureFile = parts[1];
break;
case "SearchMode":
param.SearchMode = Convert.ToInt32(parts[1]);
break;
case "Tda":
param.Tda = parts[1];
break;
case "PrecursorIonTolerancePpm":
param.PrecursorTolerancePpm = new Tolerance(Convert.ToDouble(parts[1]), ToleranceUnit.Ppm);
break;
case "ProductIonTolerancePpm":
param.ProductIonTolerancePpm = 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.Add(ParseModification(parts[1]));
break;
}
}
if (param.PrecursorTolerancePpm == null && param.ProductIonTolerancePpm != null)
{
param.PrecursorTolerancePpm = param.ProductIonTolerancePpm;
}
if (param.PrecursorTolerancePpm != null && param.ProductIonTolerancePpm == null)
{
param.ProductIonTolerancePpm = param.PrecursorTolerancePpm;
}
return(param);
}