public void TestLoadDatabase(string path, int expectedNumberOfTargets)
{
var reader = new SqLiteTargetDatabaseReader();
var database = reader.ReadDb(GetTestSuiteDataPath(path));
var numberOfTargets = database.ConsensusTargets.Count;
Assert.AreEqual(expectedNumberOfTargets, numberOfTargets);
}
public void BackgroundWorker_DoWork(object sender, DoWorkEventArgs e)
{
//mAbortRequested = false;
var targetDatabaseReader = new SqLiteTargetDatabaseReader();
//Database = targetDatabaseReader.Read(DatabaseFileName);
}
/// <summary>
/// Load an existing MTDB database into a TargetDatabase
/// </summary>
/// <param name="path">Path to MTDB file</param>
/// <returns></returns>
public static TargetDatabase LoadDB(string path)
{
if (File.Exists(path) && Path.GetExtension(path) == ".mtdb")
{
var mtdbReader = new SqLiteTargetDatabaseReader();
return(mtdbReader.ReadDb(path));
}
return(new TargetDatabase());
}
private void ReadDatabase()
{
var dlg = new OpenFileDialog
{
Filter = "Mass Tag Database (*.mtdb)|*.mtdb|AllFile (*.*)|*.*",
Title = "Load MTDB from file",
InitialDirectory = RestoreDirectory,
RestoreDirectory = true
};
if (dlg.ShowDialog() == true)
{
var reader = new SqLiteTargetDatabaseReader();
//AnalysisJobViewModel.Database = reader.Read(dlg.FileName);
}
}
private void ProcessAnalysisJob(object param)
{
// Insert database save location here
var saveDatabaseDialog = new SaveFileDialog();
if (Options.DatabaseType != DatabaseType.NotSaved)
{
if (RestoreDirectory == null)
{
RestoreDirectory = "C:\\";
}
saveDatabaseDialog.InitialDirectory = RestoreDirectory;
saveDatabaseDialog.RestoreDirectory = true;
if (Options.DatabaseType == DatabaseType.SQLite)
{
saveDatabaseDialog.Filter = "Mass Tag Database (*.mtdb)|*.mtdb|All Files (*.*)|*.*";
saveDatabaseDialog.Title = "Save to MTDB";
}
else
{
saveDatabaseDialog.Filter = "Access Database (*.mdb)|*.mdb|All Files (*.*)|*.*";
saveDatabaseDialog.Title = "Save to Access Database";
}
saveDatabaseDialog.ShowDialog();
if (saveDatabaseDialog.FileName != "")
{
RestoreDirectory = Path.GetDirectoryName(saveDatabaseDialog.FileName);
SavedDatabasePath = saveDatabaseDialog.FileName;
}
}
DateTime start = DateTime.Now;
var result = ProcessAnalysisTargets();
OnAnalysisJobProcessed(new MtdbResultChangedEventArgs(result));
DateTime end = DateTime.Now;
Console.WriteLine("Analysis processed after " + (end - start));
if (File.Exists(SavedDatabasePath))
{
ITargetDatabaseReader reader;
IEnumerable <LcmsDataSet> databaseDatasets = null;
var loaded = false;
MessageBoxResult errorResult = MessageBoxResult.OK;
if (SavedDatabasePath.EndsWith("mtdb"))
{
reader = new SqLiteTargetDatabaseReader();
}
else
{
reader = new AccessTargetDatabaseReader();
}
try
{
databaseDatasets = reader.Read(SavedDatabasePath);
loaded = true;
}
catch (Exception)
{
errorResult = MessageBox.Show(string.Format("{0} does not contain valid data to be imported into MTDBCreator", SavedDatabasePath),
"Error loading file", MessageBoxButton.OKCancel, MessageBoxImage.Exclamation);
}
if (loaded)
{
foreach (var dataset in databaseDatasets)
{
var exists = false;
var priorAnalysis = new AnalysisJobItem(dataset.Name, dataset.Tool);
priorAnalysis.DataSet = dataset;
foreach (var item in AnalysisJobItems)
{
if (item.Title == priorAnalysis.Title)
{
item.DataSet = dataset;
exists = true;
}
}
if (!exists)
{
AnalysisJobItems.Add(priorAnalysis);
}
}
}
else if (errorResult == MessageBoxResult.Cancel)
{
// User cancelled processing
var squelch = 1;
squelch++;
return;
}
}
if (result != null && param == null)
{
DateTime procStart = DateTime.Now;
result = ProcessAnalysisDatabase();
if (result == null && BackgroundWorkProcessHelper.MostRecentResult != null)
{
// This condition will be true if MultithreadingEnabled = false
result = BackgroundWorkProcessHelper.MostRecentResult;
if (Database == null && result is TargetDatabase)
{
Database = (TargetDatabase)result;
}
}
OnAnalysisJobProcessed(new MtdbResultChangedEventArgs(result));
end = DateTime.Now;
Console.WriteLine("Alignment processed after " + (end - start) + " total");
Console.WriteLine("Alignment took " + (end - procStart));
if (result != null && saveDatabaseDialog.FileName != "")
{
DateTime saveStart = DateTime.Now;
SaveAnalysisDatabase(saveDatabaseDialog.FileName);
IsDatabaseSaved = true;
end = DateTime.Now;
Console.WriteLine("Database Save took " + (end - saveStart));
}
}
}
public MassTagDatabase LoadDatabase()
{
var database = new MassTagDatabase();
//Implement the loading / reading of the MTDB Framework objects.
var reader = new SqLiteTargetDatabaseReader();
var mtdbDatabase = reader.ReadDb(m_path);
var massTags = new List<MassTagLight>();
// Mapping objects to create unique proteins and for the mass tag database to load only those proteins for
// the given consensus targets/mass tags.
var proteinMap = new Dictionary<int, Protein>();
var massTagProteinMap = new Dictionary<int, List<Protein>>();
if (mtdbDatabase == null)
return database;
foreach (var target in mtdbDatabase.ConsensusTargets)
{
// Copy the consensus data into a mass tag light.
var tag = new MassTagLight
{
Id = target.Id,
MassMonoisotopic = target.TheoreticalMonoIsotopicMass,
NetAverage = target.AverageNet,
NetPredicted = target.PredictedNet,
PeptideSequence = target.Sequence,
NetStandardDeviation = target.StdevNet
};
// Here we create unique proteins for the mass tag copying information from the consensus target proteins.
var proteinsForMassTag = new List<Protein>();
foreach (var targetProtein in target.Proteins)
{
if (!proteinMap.ContainsKey(targetProtein.Id))
{
var newProtein = new Protein
{
Id = targetProtein.Id,
Name = targetProtein.ProteinName,
ResidueStartPosition = targetProtein.ResidueStart,
ResidueEndPosition = targetProtein.ResidueEnd
};
//TODO: Do something about the cleavage state and terminus state of a protein loaded from MTDBCreator database.
//protein.CleavageState = ??
//protein.TerminusState = ??
proteinMap.Add(newProtein.Id, newProtein);
}
var protein = proteinMap[targetProtein.Id];
proteinsForMassTag.Add(protein);
}
massTagProteinMap.Add(tag.Id, proteinsForMassTag);
massTags.Add(tag);
}
database.AddMassTagsAndProteins(massTags, massTagProteinMap);
return database;
}
/// <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);
}
public MassTagDatabase LoadDatabase()
{
var database = new MassTagDatabase();
//Implement the loading / reading of the MTDB Framework objects.
var reader = new SqLiteTargetDatabaseReader();
var mtdbDatabase = reader.ReadDb(m_path);
var massTags = new List <MassTagLight>();
// Mapping objects to create unique proteins and for the mass tag database to load only those proteins for
// the given consensus targets/mass tags.
var proteinMap = new Dictionary <int, Protein>();
var massTagProteinMap = new Dictionary <int, List <Protein> >();
if (mtdbDatabase == null)
{
return(database);
}
foreach (var target in mtdbDatabase.ConsensusTargets)
{
// Copy the consensus data into a mass tag light.
var tag = new MassTagLight
{
Id = target.Id,
MassMonoisotopic = target.TheoreticalMonoIsotopicMass,
NetAverage = target.AverageNet,
NetPredicted = target.PredictedNet,
PeptideSequence = target.Sequence,
NetStandardDeviation = target.StdevNet
};
// Here we create unique proteins for the mass tag copying information from the consensus target proteins.
var proteinsForMassTag = new List <Protein>();
foreach (var targetProtein in target.Proteins)
{
if (!proteinMap.ContainsKey(targetProtein.Id))
{
var newProtein = new Protein
{
Id = targetProtein.Id,
Name = targetProtein.ProteinName,
ResidueStartPosition = targetProtein.ResidueStart,
ResidueEndPosition = targetProtein.ResidueEnd
};
//TODO: Do something about the cleavage state and terminus state of a protein loaded from MTDBCreator database.
//protein.CleavageState = ??
//protein.TerminusState = ??
proteinMap.Add(newProtein.Id, newProtein);
}
var protein = proteinMap[targetProtein.Id];
proteinsForMassTag.Add(protein);
}
massTagProteinMap.Add(tag.Id, proteinsForMassTag);
massTags.Add(tag);
}
database.AddMassTagsAndProteins(massTags, massTagProteinMap);
return(database);
}
