/// <summary>
/// Copies the exsting database.
/// </summary>
/// <param name="filter"></param>
/// <returns></returns>
private void Filter(MassTagDatabase database, ITargetFilter filter)
{
Dictionary <int, bool> targets = new Dictionary <int, bool>();
foreach (ConsensusTarget averageTarget in database.ConsensusTargets)
{
/// Perform any filtering now...we allow the mass tag to pass if one of the targets is allowed to pass through...
bool shouldFilter = true;
foreach (Target target in averageTarget.Targets)
{
if (!filter.ShouldFilter(target))
{
shouldFilter = false;
break;
}
}
// Here we update the map, so that if it was filtered above, then we mark it As such so we dont add the protein data
if (!targets.ContainsKey(averageTarget.Id))
{
targets.Add(averageTarget.Id, shouldFilter);
}
targets[averageTarget.Id] = shouldFilter;
if (shouldFilter)
{
continue;
}
m_massTags.Add(averageTarget);
}
AggregateProteins();
}
/// <summary>
/// Copy constructor based on an existing database and a filtering mechanism.
/// </summary>
/// <param name="database"></param>
/// <param name="filter"></param>
public MassTagDatabase(MassTagDatabase database, ITargetFilter filter)
{
MetaData = new List <Analysis>();
m_massTags = new List <ConsensusTarget>();
m_massTagMap = new Dictionary <string, ConsensusTarget>();
Proteins = new List <Protein>();
Filter(database, filter);
}
/// <summary>
/// Threaded entry point for creating a mass tag database.
/// </summary>
private void CreateDatabaseInternal()
{
p_database = CreateDatabaseInternal(p_options, p_analyses);
if (p_database == null)
{
return;
}
if (DatabaseCreated != null)
{
DatabaseCreated(this, new DatabaseCreatedEventArgs(p_database));
}
}
public DatabaseCreatedEventArgs(MassTagDatabase database)
{
Database = database;
}
/// <summary>
/// Processes a list of dataset objects and returns a MTDB.
/// </summary>
private MassTagDatabase CreateDatabaseInternal(
Options options,
List <Analysis> analysisDescriptions)
{
MassTagDatabase massTagDatabase = new MassTagDatabase();
IRetentionTimePredictor predictor = RetentionTimePredictorFactory.CreatePredictor(options.PredictorType);
bool success = true;
// Analyze each of the datasets, putting the results into the mass tag database
// To expedite this process, only analyze if the analysis has not already been processed.
int analysisNumber = 1;
foreach (Analysis analysis in analysisDescriptions)
{
try
{
if (analysis.ProcessedState != ProcessingState.Processed)
{
ProcessAnalysisJobInternal(analysis, options, predictor);
}
massTagDatabase.AddResults(analysis.Targets,
options.Regression,
predictor);
massTagDatabase.AddMetaData(analysis);
GC.Collect();
GC.WaitForPendingFinalizers();
GC.Collect();
GC.WaitForPendingFinalizers();
if (AnalysisCompleted != null)
{
AnalysisCompleted(this, new AnalysisCompletedEventArgs(analysisNumber++, analysisDescriptions.Count, analysis));
}
}
catch (IOException ex)
{
analysis.ProcessedState = ProcessingState.NotProcessed;
success = false;
OnError(string.Format("Failed to open the analysis file {0} - {1}", analysis.FilePath, ex.Message));
break;
}
catch (AnalysisToolException ex)
{
analysis.ProcessedState = ProcessingState.NotProcessed;
success = false;
OnError(string.Format("The analysis failed for {0} - {1}", analysis.Name, ex.Message));
break;
}
catch (Exception ex)
{
analysis.ProcessedState = ProcessingState.NotProcessed;
success = false;
OnError(string.Format("The analysis failed for {0} - {1}", analysis.Name, ex.Message));
break;
}
}
if (success)
{
massTagDatabase.FinalizeDatabase();
}
else
{
massTagDatabase = null;
if (this.AnalysisFailed != null)
{
AnalysisFailed(this, new DatabaseCreatedEventArgs(null));
}
}
return(massTagDatabase);
}
