public ScatterSeries MakePredictedAnalysisScatterSeries(AnalysisJobItem analysisJobItem, Options options)
{
var color = m_SeriesColorDictionary[analysisJobItem.FilePath];
var scatterSeries = new ScatterSeries
{
MarkerSize = 2,
// Use Cross MarkerType and MarkerStroke (instead of MarkerFill) to improve the graphing performance
MarkerStroke = OxyColor.FromArgb(color.A, color.R, color.G, color.B),
MarkerType = MarkerType.Cross,
Title = analysisJobItem.Title,
Tag = analysisJobItem,
};
foreach (var evidence in analysisJobItem.DataSet.Evidences)
{
var filter = AlignmentFilterFactory.Create(analysisJobItem.Format, options);
if (!filter.ShouldFilter(evidence))
{
var scatterPoint = new ScatterPoint(evidence.ObservedNet, evidence.PredictedNet)
{
Tag = evidence
};
scatterSeries.Points.Add(scatterPoint);
}
}
return(scatterSeries);
}
/// <summary>
/// Process Analysis Job Items according to their individual file types
/// </summary>
/// <param name="analysisJobItems">Analysis Job Items</param>
/// <param name="bWorker"></param>
/// <returns>Processed Analysis Job Items</returns>
public IEnumerable <AnalysisJobItem> Process(IEnumerable <AnalysisJobItem> analysisJobItems, BackgroundWorker bWorker)
{
// analysisJobItems should have LcmsDataSet field be null
m_abortRequested = false;
m_currentItem = 0;
m_totalItems = analysisJobItems.Count();
foreach (var jobItem in analysisJobItems)
{
if (bWorker.CancellationPending || m_abortRequested)
{
break;
}
OnProgressChanged(new MtdbProgressChangedEventArgs(m_currentItem, m_totalItems, jobItem));
m_currentJob = jobItem;
m_analysisReader = PhrpReaderFactory.Create(jobItem.FilePath, ProcessorOptions);
m_analysisReader.ProgressChanged += analysisReader_ProgressChanged;
// Reads the jobItem using the reader returned by the Reader Factory
jobItem.DataSet = m_analysisReader.Read(jobItem.FilePath);
m_currentItem++;
}
return(analysisJobItems);
}
public LineAnnotation MakeRegressionLineAnnotation(AnalysisJobItem analysisJobItem)
{
return(new LineAnnotation
{
Type = LineAnnotationType.LinearEquation,
Color = OxyColors.Black,
Intercept = analysisJobItem.DataSet.RegressionResult.Intercept,
Slope = analysisJobItem.DataSet.RegressionResult.Slope,
StrokeThickness = 2,
Layer = AnnotationLayer.AboveSeries,
LineStyle = LineStyle.Solid,
Tag = analysisJobItem
});
}
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));
}
}
}
/// <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);
}
