public void outputToSqlite_uimf_test1()
{
List <Run> runcoll = new List <Run>();
Run run = new UIMFRun(uimfFile1);
runcoll.Add(run);
FrameSetCollectionCreator fsc = new FrameSetCollectionCreator(run, 800, 809, 3, 1);
fsc.Create();
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 200, 220, 9, 1);
sscc.Create();
Task msgen = new UIMF_MSGenerator();
Task peakDetector = new DeconToolsPeakDetector();
Task decon = new RapidDeconvolutor();
Task driftTimeExtractor = new DeconTools.Backend.ProcessingTasks.UIMFDriftTimeExtractor();
Task origIntensExtr = new DeconTools.Backend.ProcessingTasks.OriginalIntensitiesExtractor();
Task ticExtractor = new DeconTools.Backend.ProcessingTasks.UIMF_TICExtractor();
Task scanResultUpdater = new ScanResultUpdater();
Task sqliteExporter = new DeconTools.Backend.ProcessingTasks.ResultExporters.ScanResultExporters.UIMFScanResult_SqliteExporter(uimf_Sqlite_ScanResultOutputFile1);
Stopwatch sw;
foreach (FrameSet frame in ((UIMFRun)run).FrameSetCollection.FrameSetList)
{
((UIMFRun)run).CurrentFrameSet = frame;
foreach (ScanSet scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
ticExtractor.Execute(run.ResultCollection);
scanResultUpdater.Execute(run.ResultCollection);
driftTimeExtractor.Execute(run.ResultCollection);
origIntensExtr.Execute(run.ResultCollection);
sw = new Stopwatch();
sw.Start();
sqliteExporter.Execute(run.ResultCollection);
sw.Stop();
if (sw.ElapsedMilliseconds > 10)
{
Console.WriteLine("SqliteExporter execution time = \t" + sw.ElapsedMilliseconds);
}
}
}
}
public void outputToText_uimf_test1()
{
if (File.Exists(uimf_text_IsosResultOutputFile1))
{
File.Delete(uimf_text_IsosResultOutputFile1);
}
List <Run> runcoll = new List <Run>();
Run run = new UIMFRun(uimfFile1);
runcoll.Add(run);
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 200, 240, 9, 1, false);
sscc.Create();
FrameSetCollectionCreator fsc = new FrameSetCollectionCreator(run, 800, 801, 3, 1);
fsc.Create();
Task msgen = new UIMF_MSGenerator();
Task peakDetector = new DeconToolsPeakDetector();
Task decon = new HornDeconvolutor();
Task driftTimeExtractor = new DeconTools.Backend.ProcessingTasks.UIMFDriftTimeExtractor();
Task origIntensExtr = new DeconTools.Backend.ProcessingTasks.OriginalIntensitiesExtractor();
Task isosExporter = new DeconTools.Backend.ProcessingTasks.ResultExporters.IsosResultExporters.UIMFIsosResultTextFileExporter(uimf_text_IsosResultOutputFile1, 1000000);
Task flagger = new ResultValidatorTask();
Stopwatch sw;
foreach (FrameSet frame in ((UIMFRun)run).FrameSetCollection.FrameSetList)
{
((UIMFRun)run).CurrentFrameSet = frame;
foreach (ScanSet scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
flagger.Execute(run.ResultCollection);
driftTimeExtractor.Execute(run.ResultCollection);
origIntensExtr.Execute(run.ResultCollection);
sw = new Stopwatch();
sw.Start();
isosExporter.Execute(run.ResultCollection);
sw.Stop();
if (sw.ElapsedMilliseconds > 10)
{
Console.WriteLine("execution time = \t" + sw.ElapsedMilliseconds);
}
}
}
Assert.AreEqual(true, File.Exists(uimf_text_IsosResultOutputFile1));
FileInfo fi = new FileInfo(uimf_text_IsosResultOutputFile1);
Assert.AreEqual(99743, fi.Length);
Console.Write(fi.Length);
}
public void msGeneratorSummingTest1()
{
Run run = new UIMFRun(uimfFilePath3);
int startFrame = 800;
int stopFrame = 802;
int numFramesSummed = 3;
int numScansSummed = 9;
FrameSetCollectionCreator framesetCreator = new FrameSetCollectionCreator(run, startFrame, stopFrame, numFramesSummed, 1);
framesetCreator.Create();
ScanSetCollectionCreator scanSetCreator = new ScanSetCollectionCreator(run, numScansSummed, 1);
scanSetCreator.Create();
ResultCollection results = new ResultCollection(run);
List <timingResult> timingResults = new List <timingResult>();
Task msgen = new UIMF_MSGenerator();
Task peakDetector = new DeconToolsPeakDetector();
Task decon = new HornDeconvolutor();
Task scanResultUpdater = new ScanResultUpdater();
Task uimfTicExtractor = new UIMF_TICExtractor();
Task driftTimeExtractor = new DeconTools.Backend.ProcessingTasks.UIMFDriftTimeExtractor();
((HornDeconvolutor)decon).MinPeptideBackgroundRatio = 4;
foreach (FrameSet frameset in ((UIMFRun)run).FrameSetCollection.FrameSetList)
{
System.Diagnostics.Stopwatch sw = new System.Diagnostics.Stopwatch();
((UIMFRun)run).CurrentFrameSet = frameset;
foreach (ScanSet scanset in run.ScanSetCollection.ScanSetList)
{
sw.Reset();
timingResult timeresult = new timingResult();
timeresult.frameNum = frameset.PrimaryFrame;
timeresult.scanNum = scanset.PrimaryScanNumber;
sw.Start();
run.CurrentScanSet = scanset;
msgen.Execute(results);
timeresult.msGenTime = sw.ElapsedMilliseconds;
sw.Reset();
sw.Start();
peakDetector.Execute(results);
timeresult.peakDetectorTime = sw.ElapsedMilliseconds;
sw.Reset();
sw.Start();
decon.Execute(results);
timeresult.deconTime = sw.ElapsedMilliseconds;
sw.Reset();
sw.Start();
scanResultUpdater.Execute(results);
timeresult.resultUpdaterTime = sw.ElapsedMilliseconds;
sw.Reset();
sw.Start();
uimfTicExtractor.Execute(results);
timeresult.ticExtractorTime = sw.ElapsedMilliseconds;
sw.Reset();
sw.Start();
driftTimeExtractor.Execute(results);
timeresult.driftTimeExtractorTime = sw.ElapsedMilliseconds;
timingResults.Add(timeresult);
}
}
//reportTimingEachFrameEachScan(timingResults);
Console.WriteLine("Total _isos = " + results.ResultList.Count);
Console.WriteLine("PeptideBR = " + ((HornDeconvolutor)decon).MinPeptideBackgroundRatio);
Console.WriteLine();
Console.WriteLine();
Console.WriteLine();
reportTiming_FrameAggregate(timingResults, startFrame, stopFrame);
Project.Reset();
}