public void test1()
        {
            Run run = new XCaliburRun(xcaliburTestfile);

            List <MassTag> mass_tagList = TestUtilities.CreateTestMassTagList();
            MassTag        mt           = mass_tagList[0];

            run.CurrentScanSet = new ScanSet(9017, new int[] { 9010, 9017, 9024 });
            run.CurrentMassTag = mt;


            MSGeneratorFactory msgenFactory = new MSGeneratorFactory();
            Task msgen = msgenFactory.CreateMSGenerator(run.MSFileType);

            DeconToolsV2.Peaks.clsPeakProcessorParameters peakParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(2, 1.3, true, DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC);
            Task mspeakDet = new DeconToolsPeakDetector(peakParams);

            Task theorFeatureGen       = new TomTheorFeatureGenerator();
            Task targetedFeatureFinder = new BasicTFF(0.01);

            IsotopicProfileFitScoreCalculator fitScoreCalc = new IsotopicProfileFitScoreCalculator();
            Task exporter = new BasicMTResultSQLiteExporter(exporterOutputFile1);



            msgen.Execute(run.ResultCollection);

            //run.XYData.Display();

            mspeakDet.Execute(run.ResultCollection);
            theorFeatureGen.Execute(run.ResultCollection);
            targetedFeatureFinder.Execute(run.ResultCollection);
            fitScoreCalc.Execute(run.ResultCollection);
            exporter.Execute(run.ResultCollection);
            exporter.Cleanup();

            MassTagResultBase result = run.ResultCollection.GetMassTagResult(mt);

            TestUtilities.DisplayIsotopicProfileData(result.IsotopicProfile);
        }
예제 #2
0
        public void test1()
        {
            Run run = new XCaliburRun(xcaliburTestfile);
            MassTagCollection        massTagColl  = new MassTagCollection();
            MassTagIDGenericImporter mtidImporter = new MassTagIDGenericImporter(cysteineMassTagSourceFile1, '\t');

            mtidImporter.Import(massTagColl);

            MassTagFromSqlDBImporter importer = new MassTagFromSqlDBImporter("MT_Shewanella_ProdTest_P352", "porky");

            importer.Import(massTagColl);

            Assert.AreEqual(737, massTagColl.MassTagIDList.Count);

            Assert.AreEqual(826, massTagColl.MassTagList.Count);

            ChromAlignerUsingVIPERInfo chromAligner = new ChromAlignerUsingVIPERInfo();

            chromAligner.Execute(run);

            PeakImporterFromText peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(xcaliburAllPeaksFile);

            peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);

            Task peakChromGen = new PeakChromatogramGenerator(20);

            Task smoother     = new DeconTools.Backend.ProcessingTasks.Smoothers.DeconToolsSavitzkyGolaySmoother(11, 11, 2);
            Task peakDet      = new DeconTools.Backend.ProcessingTasks.PeakDetectors.ChromPeakDetector(0.5, 0.5);
            Task chromPeakSel = new DeconTools.Backend.ProcessingTasks.ChromPeakSelector(1, 0.01, Globals.PeakSelectorMode.CLOSEST_TO_TARGET);

            MSGeneratorFactory msgenFactory = new MSGeneratorFactory();
            Task msgen = msgenFactory.CreateMSGenerator(run.MSFileType);


            DeconToolsV2.Peaks.clsPeakProcessorParameters peakParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(2, 0.75, true, DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC);
            Task mspeakDet             = new DeconToolsPeakDetector(peakParams);
            Task theorFeatureGen       = new TomTheorFeatureGenerator();
            Task targetedFeatureFinder = new BasicTFF(6);
            Task exporter = new BasicMTResultSQLiteExporter(cysteineAnalysisOutput1);


            IsotopicProfileFitScoreCalculator fitScoreCalc = new IsotopicProfileFitScoreCalculator();

            int         successCounter = 0;
            List <long> timingResults  = new List <long>();

            foreach (MassTag mt in massTagColl.MassTagList)
            {
                run.CurrentMassTag = mt;
                mt.MZ = mt.MonoIsotopicMass / mt.ChargeState + Globals.PROTON_MASS;

                Console.WriteLine();
                Console.WriteLine();
                Console.WriteLine("------------------- MassTag = " + mt.ID + "---------------------------");
                Console.WriteLine("monoMass = " + mt.MonoIsotopicMass.ToString("0.0000") + "; monoMZ = " + mt.MZ.ToString("0.0000") + "; ChargeState = " + mt.ChargeState + "; NET = " + mt.NETVal.ToString("0.000") + "; Sequence = " + mt.PeptideSequence + "\n");


                Stopwatch sw = new Stopwatch();
                sw.Start();
                try
                {
                    peakChromGen.Execute(run.ResultCollection);
                    smoother.Execute(run.ResultCollection);
                    peakDet.Execute(run.ResultCollection);
                    chromPeakSel.Execute(run.ResultCollection);
                    msgen.Execute(run.ResultCollection);
                    mspeakDet.Execute(run.ResultCollection);
                    theorFeatureGen.Execute(run.ResultCollection);
                    targetedFeatureFinder.Execute(run.ResultCollection);
                    fitScoreCalc.Execute(run.ResultCollection);
                    MassTagResultBase massTagResult = run.ResultCollection.MassTagResultList[mt];
                    massTagResult.DisplayToConsole();


                    Console.WriteLine("------------------------------ end --------------------------");
                }
                catch (Exception ex)
                {
                    Console.WriteLine("Task failed. Message: " + ex.Message + ex.StackTrace);
                }
                sw.Stop();
                timingResults.Add(sw.ElapsedMilliseconds);

                if (mt == massTagColl.MassTagList.Last())
                {
                    exporter.Execute(run.ResultCollection);
                }
            }

            exporter.Cleanup();

            //List<IMassTagResult> successfulResults = run.ResultCollection.GetSuccessfulMassTagResults();

            foreach (long tr in timingResults)
            {
                Console.WriteLine(tr);
            }
            Console.WriteLine("-------- Analysis time for all MTs = " + timingResults.Sum());
            Console.WriteLine("-------- Average time for each MT = " + timingResults.Average());

            Console.WriteLine();
        }