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 BackgroundWorker_DoWork(object sender, DoWorkEventArgs e)
{
mAbortRequested = false;
ITargetDatabaseWriter targetDatabaseWriter = new SqLiteTargetDatabaseWriter();
if (DatabaseOptions.DatabaseType != DatabaseType.Access)
{
targetDatabaseWriter = new SqLiteTargetDatabaseWriter();
}
else
{
targetDatabaseWriter = new AccessTargetDatabaseWriter();
}
targetDatabaseWriter.ProgressChanged += targetDatabaseWriter_ProgressChanged;
targetDatabaseWriter.Write(Database, DatabaseOptions, DatabaseFileName);
}
public void TestWriteDatabase(string path, int numberOfTargets, int numberOfEvidences)
{
var reader = new SqLiteTargetDatabaseWriter();
var options = new Options();
var database = new TargetDatabase();
var proteinCount = 1;
var evidenceCount = 1;
for (var i = 1; i <= numberOfTargets; i++)
{
var target = new ConsensusTarget {
Id = i
};
var protein = new ProteinInformation
{
ProteinName = "SO_Test" + proteinCount++,
CleavageState = clsPeptideCleavageStateCalculator.ePeptideCleavageStateConstants.Full,
TerminusState = clsPeptideCleavageStateCalculator.ePeptideTerminusStateConstants.ProteinNTerminus,
};
protein.Consensus.Add(target);
for (var j = 1; j <= numberOfEvidences; j++)
{
var evidence = new Evidence
{
AnalysisId = j,
Charge = 1,
Id = evidenceCount,
CleanPeptide = "MIKEDEGAN" + evidenceCount,
Sequence = "BIGBIRD" + evidenceCount,
Mz = 405,
Scan = evidenceCount++,
PeptideInfo = new TargetPeptideInfo()
};
evidence.AddProtein(protein);
target.AddEvidence(evidence);
}
target.AddProtein(protein);
target.CalculateStatistics();
database.ConsensusTargets.Add(target);
}
reader.Write(database, options, GetTestSuiteDataPath(path));
}
/// <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);
}
