public void TestLcmsWarpWrite(params string[] paths)
{
var fullPaths = new List <string>();
var fullOutputPaths = new List <string>();
foreach (var path in paths)
{
fullPaths.Add(GetPath(path));
fullOutputPaths.Add(GetOutputPath(path));
}
var options = new Options
{
RegressionType = RegressionType.MixtureRegression
};
var analysisProcessor = new AnalysisJobProcessor(options);
var individualJobs = fullPaths.Select(path => new AnalysisJobItem(path, LcmsIdentificationTool.MsgfPlus)).ToList();
var bWorker = new BackgroundWorker();
var jobs = analysisProcessor.Process(individualJobs, bWorker);
var databaseProcess = new MtdbProcessor(options);
databaseProcess.Process(jobs.Select(job => job.DataSet).ToList(), bWorker);
}
public void TestWriteReal(params string[] paths)
{
var fullPaths = new List <string>();
var fullOutputPaths = new List <string>();
foreach (var path in paths)
{
fullPaths.Add(GetPath(path));
fullOutputPaths.Add(GetOutputPath(path));
}
var options = new Options();
var analysisProcessor = new AnalysisJobProcessor(options);
var individualJobs = fullPaths.Select(path => new AnalysisJobItem(path, LcmsIdentificationTool.MsgfPlus)).ToList();
var bWorker = new BackgroundWorker();
var jobs = analysisProcessor.Process(individualJobs, bWorker);
var databaseProcess = new MtdbProcessor(options);
var database = databaseProcess.Process(jobs.Select(job => job.DataSet).ToList(), bWorker);
var writer = new SqLiteTargetDatabaseWriter();
writer.Write(database, options, GetTestSuiteDataPath(@"Output.mtdb"));
}
public void LinearRegression(string jobDirectory, string jobList, int numJobs)
{
var jobDirectoryPath = GetPath(jobDirectory);
var jobListPath = GetPath(jobList);
var num = 0;
var options = new Options();
PeptideCache.Clear();
var dataSets = new List <LcmsDataSet>();
using (var sr = new StreamReader(jobListPath))
{
var pathName = sr.ReadLine();
while (pathName != null && num < numJobs)
{
pathName = Path.Combine(jobDirectoryPath, pathName);
var reader = PhrpReaderFactory.Create(pathName, options);
dataSets.Add(reader.Read(pathName));
pathName = sr.ReadLine();
num++;
}
}
var processor = new MtdbProcessor(options);
processor.Process(dataSets, new BackgroundWorker());
foreach (var set in dataSets)
{
Assert.AreNotEqual(set.RegressionResult.RSquared, 0);
// Set to 1.000001 due to (for some reason) RSquared occasionally
// being calculated as 1.00000000000044
Assert.Less(set.RegressionResult.RSquared, 1.000001);
}
}
public void BackgroundWorker_DoWork(object sender, DoWorkEventArgs e)
{
mAbortRequested = false;
var mtdbProcessor = new MtdbProcessor(m_analysisJobViewModel.Options);
mtdbProcessor.AlignmentComplete += mtdbProcessor_AlignmentComplete;
mtdbProcessor.ProgressChanged += mtdbProcessor_ProgressChanged;
HostProcessWindow.MainBackgroundWorker.ReportProgress(0);
try
{
e.Result =
mtdbProcessor.Process(
m_analysisJobViewModel.AnalysisJobItems.Select(job => job.DataSet).ToList(), HostProcessWindow.MainBackgroundWorker);
if (HostProcessWindow.MainBackgroundWorker.CancellationPending || mAbortRequested)
{
e.Cancel = true;
}
}
catch (Exception ex)
{
e.Result = ex;
}
}
/// <summary>
/// Create a MTDB with the given files
/// </summary>
/// <param name="paths">Paths to the files to process</param>
/// <param name="dbFileName">Name of MTDB to create</param>
/// <returns></returns>
public static TargetDatabase CreateDB(List <string> paths, string dbFileName)
{
var options = new Options();
var analysisProcessor = new AnalysisJobProcessor(options);
var mtdbProcessor = new MtdbProcessor(options);
var bWorker = new BackgroundWorker();
var writer = new SqLiteTargetDatabaseWriter();
var reader = new SqLiteTargetDatabaseReader();
var existingDatabase = new TargetDatabase();
IEnumerable <LcmsDataSet> priorDataSets = new List <LcmsDataSet>();
if (File.Exists(dbFileName))
{
priorDataSets = reader.Read(dbFileName);
existingDatabase = reader.ReadDb(dbFileName);
}
var priorDatasetList = priorDataSets.Select(x => x.Name).ToList();
var listJobs = new List <AnalysisJobItem>();
foreach (var path in paths)
{
if (File.Exists(path))
{
var tool = DetermineTool(path);
var jobName = path.Split('\\').Last();
if (tool == LcmsIdentificationTool.NOT_SUPPORTED)
{
Console.WriteLine(jobName + " is not a supported LCMS format for MTDBCreator;\nExcluding this file from MTDB creation\n");
}
else if (priorDatasetList.Any(x => jobName.Contains(x)))
{
Console.WriteLine(jobName + " is part of prior analysis;\nExcluding from reading portion of MTDB creation\n");
}
else
{
var individualJob = new AnalysisJobItem(path, tool);
listJobs.Add(individualJob);
}
}
else
{
Console.WriteLine(path + " does not exist;\nExcluding this file in MTDB creation\n");
}
}
if (listJobs.Count != 0)
{
var processedjobs = analysisProcessor.Process(listJobs, bWorker);
var datasetList = processedjobs.Select(job => job.DataSet).ToList();
if (priorDataSets != null)
{
datasetList.AddRange(priorDataSets);
}
var database = mtdbProcessor.Process(datasetList, bWorker);
writer.Write(database, options, dbFileName);
return(database);
}
return(existingDatabase);
}
