public void Write()
{
var outputFilePath = Path.Combine(OutputDir, Path.GetFileNameWithoutExtension(SpecFilePath) + ParameterFileExtension);
using (var writer = new StreamWriter(outputFilePath))
{
writer.WriteLine("SpecFile\t" + Path.GetFileName(SpecFilePath));
writer.WriteLine("DatabaseFile\t" + Path.GetFileName(DatabaseFilePath));
writer.WriteLine("FeatureFile\t{0}", !string.IsNullOrWhiteSpace(FeatureFilePath) ? Path.GetFileName(FeatureFilePath) : Path.GetFileName(MassSpecDataReaderFactory.ChangeExtension(SpecFilePath, ".ms1ft")));
writer.WriteLine("InternalCleavageMode\t" + InternalCleavageMode);
writer.WriteLine("Tag-based search\t" + TagBasedSearch);
writer.WriteLine("Tda\t" + (TargetDecoySearchMode == DatabaseSearchMode.Both ? "Target+Decoy" : TargetDecoySearchMode.ToString()));
writer.WriteLine("PrecursorIonTolerancePpm\t" + PrecursorIonTolerancePpm);
writer.WriteLine("ProductIonTolerancePpm\t" + ProductIonTolerancePpm);
writer.WriteLine("MinSequenceLength\t" + MinSequenceLength);
writer.WriteLine("MaxSequenceLength\t" + MaxSequenceLength);
writer.WriteLine("MinPrecursorIonCharge\t" + MinPrecursorIonCharge);
writer.WriteLine("MaxPrecursorIonCharge\t" + MaxPrecursorIonCharge);
writer.WriteLine("MinProductIonCharge\t" + MinProductIonCharge);
writer.WriteLine("MaxProductIonCharge\t" + MaxProductIonCharge);
writer.WriteLine("MinSequenceMass\t" + MinSequenceMass);
writer.WriteLine("MaxSequenceMass\t" + MaxSequenceMass);
writer.WriteLine("MaxDynamicModificationsPerSequence\t" + MaxDynamicModificationsPerSequence);
foreach (var searchMod in Modifications)
{
writer.WriteLine("Modification\t" + searchMod);
}
}
}
public void Display()
{
Console.WriteLine("MaxThreads: " + MaxNumThreads);
foreach (var specFilePath in SpecFilePaths)
{
Console.WriteLine("SpectrumFilePath: " + specFilePath);
}
Console.WriteLine("DatabaseFilePath: " + DatabaseFilePath);
Console.WriteLine("FeatureFilePath: {0}", FeatureFilePath ?? "N/A");
Console.WriteLine("OutputDir: " + OutputDir);
Console.WriteLine("InternalCleavageMode: " + InternalCleavageMode);
Console.WriteLine("Tag-based search: " + TagBasedSearch);
Console.WriteLine("Tda: " + (TargetDecoySearchMode == DatabaseSearchMode.Both ? "Target+Decoy" : TargetDecoySearchMode.ToString()));
Console.WriteLine("PrecursorIonTolerancePpm: " + PrecursorIonTolerancePpm);
Console.WriteLine("ProductIonTolerancePpm: " + ProductIonTolerancePpm);
Console.WriteLine("MinSequenceLength: " + MinSequenceLength);
Console.WriteLine("MaxSequenceLength: " + MaxSequenceLength);
Console.WriteLine("MinPrecursorIonCharge: " + MinPrecursorIonCharge);
Console.WriteLine("MaxPrecursorIonCharge: " + MaxPrecursorIonCharge);
Console.WriteLine("MinProductIonCharge: " + MinProductIonCharge);
Console.WriteLine("MaxProductIonCharge: " + MaxProductIonCharge);
Console.WriteLine("MinSequenceMass: " + MinSequenceMass);
Console.WriteLine("MaxSequenceMass: " + MaxSequenceMass);
Console.WriteLine("MaxDynamicModificationsPerSequence: " + MaxDynamicModificationsPerSequence);
Console.WriteLine("Modifications: ");
foreach (var searchMod in Modifications)
{
Console.WriteLine(searchMod);
}
if (!string.IsNullOrWhiteSpace(FeatureFilePath))
{
Console.WriteLine("Getting MS1 features from " + FeatureFilePath);
}
if (ScanNumbers != null && ScanNumbers.Any())
{
Console.WriteLine("Processing specific MS2 scans:");
Console.WriteLine(string.Join(", ", ScanNumbers));
}
}
