public void ForJohnJacobs()
{
const string myfht = @"C:\DMS_WorkDir\Step_1_ASCORE\U54_HPp1_LoBMI_NS_11_5Sep08_Draco_08-07-15_xt.txt";
const string mydta = @"C:\DMS_WorkDir\Step_1_ASCORE\dtas\U54_HPp1_LoBMI_NS_11_5Sep08_Draco_08-07-15_dta.txt";
const string mypar = @"C:\DMS_WorkDir\Step_1_ASCORE\DynMWPYOx_EmH20_QmNH3_cid.xml";
var peptideMassCalculator = GetDefaultPeptideMassCalculator();
PsmResultsManager dataman = new XTandemFHT(myfht);
//DtaManager dta = new DtaManager(mydta);
var spectraCache = new SpectraManagerCache(peptideMassCalculator);
spectraCache.OpenFile(mydta);
var par = new ParameterFileManager(mypar);
const string fileOutput = @"C:\DMS_WorkDir\Step_1_ASCORE\U54_HPp1_LoBMI_NS_11_5Sep08_Draco_08-07-15_xt_ascore.txt";
var ascoreEngine = new AScore_DLL.AScoreProcessor();
//ascoreEngine.AlgorithmRun(dta, dataman, par, fileOutput);
ascoreEngine.RunAScoreOnSingleFile(spectraCache, dataman, par, fileOutput);
}
/// <summary>
/// Configure and run the AScore algorithm
/// </summary>
/// <param name="ascoreOptions"></param>
/// <returns></returns>
public int RunAScore(AScoreOptions ascoreOptions)
{
var paramManager = new ParameterFileManager(ascoreOptions.AScoreParamFile);
RegisterEvents(paramManager);
Console.WriteLine();
if (paramManager.DynamicMods.Count > 0 || paramManager.StaticMods.Count > 0)
{
OnStatusEvent("Loaded modifications from: " + ascoreOptions.AScoreParamFile);
foreach (var mod in paramManager.StaticMods)
{
OnStatusEvent(Utilities.GetModDescription("Static, ", mod));
}
foreach (var mod in paramManager.DynamicMods)
{
OnStatusEvent(Utilities.GetModDescription("Dynamic, ", mod));
}
foreach (var mod in paramManager.TerminiMods)
{
OnStatusEvent(Utilities.GetModDescription("Terminus, ", mod));
}
Console.WriteLine();
}
PsmResultsManager psmResultsManager;
switch (ascoreOptions.SearchType)
{
case AScoreOptions.SearchMode.XTandem:
OnStatusEvent("Caching data in " + PathUtils.CompactPathString(ascoreOptions.DbSearchResultsFile, 80));
psmResultsManager = new XTandemFHT(ascoreOptions.DbSearchResultsFile);
break;
case AScoreOptions.SearchMode.Sequest:
OnStatusEvent("Caching data in " + PathUtils.CompactPathString(ascoreOptions.DbSearchResultsFile, 80));
psmResultsManager = new SequestFHT(ascoreOptions.DbSearchResultsFile);
break;
case AScoreOptions.SearchMode.Inspect:
OnStatusEvent("Caching data in " + PathUtils.CompactPathString(ascoreOptions.DbSearchResultsFile, 80));
psmResultsManager = new InspectFHT(ascoreOptions.DbSearchResultsFile);
break;
case AScoreOptions.SearchMode.Msgfdb:
case AScoreOptions.SearchMode.Msgfplus:
OnStatusEvent("Caching data in " + PathUtils.CompactPathString(ascoreOptions.DbSearchResultsFile, 80));
if (ascoreOptions.SearchResultsType == AScoreOptions.DbSearchResultsType.Mzid)
{
if (ascoreOptions.CreateUpdatedDbSearchResultsFile)
{
psmResultsManager = new MsgfMzidFull(ascoreOptions.DbSearchResultsFile);
}
else
{
psmResultsManager = new MsgfMzid(ascoreOptions.DbSearchResultsFile);
}
}
else
{
psmResultsManager = new MsgfdbFHT(ascoreOptions.DbSearchResultsFile);
}
break;
default:
OnErrorEvent(string.Format(
"Incorrect search type: {0} , supported values are {1}",
ascoreOptions.SearchType,
string.Join(", ", Enum.GetNames(typeof(AScoreOptions.SearchMode)))
));
return(-13);
}
var peptideMassCalculator = new PeptideMassCalculator();
var spectraManager = new SpectraManagerCache(peptideMassCalculator);
RegisterEvents(spectraManager);
OnStatusEvent("Output directory: " + ascoreOptions.OutputDirectoryInfo.FullName);
var ascoreEngine = new AScoreAlgorithm();
RegisterEvents(ascoreEngine);
// Initialize the options
FilterOnMSGFScore = ascoreOptions.FilterOnMSGFScore;
// Run the algorithm
if (ascoreOptions.MultiJobMode)
{
RunAScoreWithMappingFile(ascoreOptions, spectraManager, psmResultsManager, paramManager);
}
else
{
spectraManager.OpenFile(ascoreOptions.MassSpecFile, ascoreOptions.ModSummaryFile);
RunAScoreOnSingleFile(ascoreOptions, spectraManager, psmResultsManager, paramManager);
}
OnStatusEvent("AScore Complete");
if (ascoreOptions.CreateUpdatedDbSearchResultsFile)
{
if (ascoreOptions.SearchResultsType == AScoreOptions.DbSearchResultsType.Fht)
{
CreateUpdatedFirstHitsFile(ascoreOptions);
}
else if (psmResultsManager is MsgfMzidFull mzidFull)
{
mzidFull.WriteToMzidFile(ascoreOptions.UpdatedDbSearchResultsFileName);
OnStatusEvent("Results merged; new file: " + PathUtils.CompactPathString(ascoreOptions.UpdatedDbSearchResultsFileName, 80));
}
}
return(0);
}
