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);
}
/// <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());
}
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);
}