/// <summary>
/// Read a MSPF parameter file and populate raw file and feature file.
/// </summary>
/// <param name="filePath">The path to the parameter file.</param>
private void ReadParamFile(string filePath)
{
if (!string.IsNullOrWhiteSpace(filePath))
{
var mspfParams = MsPfParameters.ReadFromFile(filePath);
var dirPath = Path.GetDirectoryName(filePath);
var raw = string.Format("{0}\\{1}", dirPath, mspfParams.PuSpecFile);
if (!string.IsNullOrWhiteSpace(mspfParams.PuSpecFile) && File.Exists(raw))
{
this.RawFilePath = raw;
}
var feature = string.Format("{0}\\{1}", dirPath, mspfParams.FeatureFile);
if (!string.IsNullOrWhiteSpace(mspfParams.FeatureFile) && File.Exists(feature))
{
this.FeatureFilePath = feature;
}
var fasta = string.Format("{0}\\{1}", dirPath, mspfParams.DatabaseFile);
if (!string.IsNullOrWhiteSpace(mspfParams.DatabaseFile) && File.Exists(fasta))
{
this.FastaFilePath = fasta;
}
}
}
/// <summary>
/// Initializes a new instance of the <see cref="SearchSettingsViewModel"/> class.
/// Initializes from <see cref="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;
}
this.SearchModifications.AddRange(
mspfParameters.Modifications.Select(
searchMod => new SearchModificationViewModel(this.dialogService)
{
SearchModification = searchMod
}));
this.MinSequenceLength = mspfParameters.MinSequenceLength;
this.MaxSequenceLength = mspfParameters.MaxSequenceLength;
this.MinSequenceMass = mspfParameters.MinSequenceMass;
this.MaxSequenceMass = mspfParameters.MaxSequenceMass;
this.MinPrecursorIonCharge = mspfParameters.MinPrecursorIonCharge;
this.MaxPrecursorIonCharge = mspfParameters.MaxPrecursorIonCharge;
this.MinProductIonCharge = mspfParameters.MinProductIonCharge;
this.MaxProductIonCharge = mspfParameters.MaxPrecursorIonCharge;
this.PrecursorIonToleranceValue = mspfParameters.PrecursorTolerancePpm.GetValue();
this.ProductIonToleranceValue = mspfParameters.ProductIonTolerancePpm.GetValue();
this.MaxDynamicModificationsPerSequence =
mspfParameters.MaxDynamicModificationsPerSequence;
}
/// <summary>
/// Set the MSPathFinder parameters given a path to a ID file.
/// </summary>
/// <param name="idFilePath">The id file path.</param>
public void SetMsPfParameters(string idFilePath)
{
try
{
this.MsPfParameters = MsPfParameters.ReadFromFile(idFilePath);
}
catch (FormatException)
{
this.dialogService.MessageBox("MsPathFinder Parameters are not properly formatted.");
}
}
private void TestTopDownSearch(string specFilePath, string dbFilePath, string outputDir, AminoAcidSet aaSet,
int minSequenceLength, int maxSequenceLength,
int minPrecursorIonCharge, int maxPrecursorIonCharge,
int minProductIonCharge, int maxProductIonCharge,
double minSequenceMass, double maxSequenceMass,
DatabaseSearchMode tda, InternalCleavageType searchMode)
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
// Search parameters
const int maxNumNTermCleavages = 1; // 30
const int maxNumCTermCleavages = 0;
const int precursorIonTolerancePpm = 10;
const int productIonTolerancePpm = 10;
var topDownOptions = new MsPfParameters(
specFilePath,
dbFilePath,
outputDir,
aaSet, "")
{
MinSequenceLength = minSequenceLength,
MaxSequenceLength = maxSequenceLength,
MaxNumNTermCleavages = maxNumNTermCleavages,
MaxNumCTermCleavages = maxNumCTermCleavages,
MinPrecursorIonCharge = minPrecursorIonCharge,
MaxPrecursorIonCharge = maxPrecursorIonCharge,
MinProductIonCharge = minProductIonCharge,
MaxProductIonCharge = maxProductIonCharge,
MinSequenceMass = minSequenceMass,
MaxSequenceMass = maxSequenceMass,
PrecursorIonTolerancePpm = precursorIonTolerancePpm,
ProductIonTolerancePpm = productIonTolerancePpm,
TargetDecoySearchMode = tda,
InternalCleavageMode = searchMode,
};
var topDownLauncher = new IcTopDownLauncher(topDownOptions);
//topDownLauncher.ForceParallel = true;
//topDownLauncher.MaxNumThreads = -1;
topDownLauncher.RunSearch(0.7);
//topDownLauncher.RunIntactProteinSearch();
}
