コード例 #1
0
        protected override MyTaskResults RunSpecific(string OutputFolder, List <DbForTask> dbFilenameList, List <string> currentRawFileList, string taskId, FileSpecificParameters[] fileSettingsList)
        {
            LoadModifications(taskId, out var variableModifications, out var fixedModifications, out var localizeableModificationTypes);

            // load proteins
            List <Protein> proteinList = LoadProteins(taskId, dbFilenameList, true, DecoyType.Reverse, localizeableModificationTypes, CommonParameters);

            // write prose settings
            ProseCreatedWhileRunning.Append("The following calibration settings were used: ");
            ProseCreatedWhileRunning.Append("protease = " + CommonParameters.DigestionParams.Protease + "; ");
            ProseCreatedWhileRunning.Append("maximum missed cleavages = " + CommonParameters.DigestionParams.MaxMissedCleavages + "; ");
            ProseCreatedWhileRunning.Append("minimum peptide length = " + CommonParameters.DigestionParams.MinPeptideLength + "; ");
            ProseCreatedWhileRunning.Append(CommonParameters.DigestionParams.MaxPeptideLength == int.MaxValue ?
                                            "maximum peptide length = unspecified; " :
                                            "maximum peptide length = " + CommonParameters.DigestionParams.MaxPeptideLength + "; ");
            ProseCreatedWhileRunning.Append("initiator methionine behavior = " + CommonParameters.DigestionParams.InitiatorMethionineBehavior + "; ");
            ProseCreatedWhileRunning.Append("fixed modifications = " + string.Join(", ", fixedModifications.Select(m => m.IdWithMotif)) + "; ");
            ProseCreatedWhileRunning.Append("variable modifications = " + string.Join(", ", variableModifications.Select(m => m.IdWithMotif)) + "; ");
            ProseCreatedWhileRunning.Append("max mods per peptide = " + CommonParameters.DigestionParams.MaxModsForPeptide + "; ");
            ProseCreatedWhileRunning.Append("max modification isoforms = " + CommonParameters.DigestionParams.MaxModificationIsoforms + "; ");
            ProseCreatedWhileRunning.Append("precursor mass tolerance = " + CommonParameters.PrecursorMassTolerance + "; ");
            ProseCreatedWhileRunning.Append("product mass tolerance = " + CommonParameters.ProductMassTolerance + ". ");
            ProseCreatedWhileRunning.Append("The combined search database contained " + proteinList.Count(p => !p.IsDecoy) + " non-decoy protein entries including " + proteinList.Count(p => p.IsContaminant) + " contaminant sequences. ");

            // start the calibration task
            Status("Calibrating...", new List <string> {
                taskId
            });
            MyTaskResults = new MyTaskResults(this)
            {
                NewSpectra           = new List <string>(),
                NewFileSpecificTomls = new List <string>()
            };

            var           myFileManager = new MyFileManager(true);
            List <string> spectraFilesAfterCalibration = new List <string>();

            for (int spectraFileIndex = 0; spectraFileIndex < currentRawFileList.Count; spectraFileIndex++)
            {
                if (GlobalVariables.StopLoops)
                {
                    break;
                }

                bool couldNotFindEnoughDatapoints = false;

                // get filename stuff
                var    originalUncalibratedFilePath = currentRawFileList[spectraFileIndex];
                var    originalUncalibratedFilenameWithoutExtension = Path.GetFileNameWithoutExtension(originalUncalibratedFilePath);
                string calibratedFilePath = Path.Combine(OutputFolder, originalUncalibratedFilenameWithoutExtension + CalibSuffix + ".mzML");

                // mark the file as in-progress
                StartingDataFile(originalUncalibratedFilePath, new List <string> {
                    taskId, "Individual Spectra Files", originalUncalibratedFilePath
                });

                CommonParameters combinedParams = SetAllFileSpecificCommonParams(CommonParameters, fileSettingsList[spectraFileIndex]);

                // load the file
                Status("Loading spectra file...", new List <string> {
                    taskId, "Individual Spectra Files"
                });

                var myMsDataFile = myFileManager.LoadFile(originalUncalibratedFilePath, CommonParameters);

                // get datapoints to fit calibration function to
                Status("Acquiring calibration data points...", new List <string> {
                    taskId, "Individual Spectra Files"
                });
                DataPointAquisitionResults acquisitionResults = null;

                for (int i = 1; i <= 5; i++)
                {
                    acquisitionResults = GetDataAcquisitionResults(myMsDataFile, originalUncalibratedFilePath, variableModifications, fixedModifications, proteinList, taskId, combinedParams, combinedParams.PrecursorMassTolerance, combinedParams.ProductMassTolerance);

                    // enough data points to calibrate?
                    if (acquisitionResults.Psms.Count >= NumRequiredPsms && acquisitionResults.Ms1List.Count > NumRequiredMs1Datapoints && acquisitionResults.Ms2List.Count > NumRequiredMs2Datapoints)
                    {
                        break;
                    }

                    if (i == 1) // failed round 1
                    {
                        CommonParameters.PrecursorMassTolerance = new PpmTolerance(20);
                        CommonParameters.ProductMassTolerance   = new PpmTolerance(50);
                    }
                    else if (i == 2) // failed round 2
                    {
                        CommonParameters.PrecursorMassTolerance = new PpmTolerance(30);
                        CommonParameters.ProductMassTolerance   = new PpmTolerance(100);
                    }
                    else if (i == 3) // failed round 3
                    {
                        CommonParameters.PrecursorMassTolerance = new PpmTolerance(40);
                        CommonParameters.ProductMassTolerance   = new PpmTolerance(150);
                    }
                    else // failed round 4
                    {
                        if (acquisitionResults.Psms.Count < NumRequiredPsms)
                        {
                            Warn("Calibration failure! Could not find enough high-quality PSMs. Required " + NumRequiredPsms + ", saw " + acquisitionResults.Psms.Count);
                        }
                        if (acquisitionResults.Ms1List.Count < NumRequiredMs1Datapoints)
                        {
                            Warn("Calibration failure! Could not find enough MS1 datapoints. Required " + NumRequiredMs1Datapoints + ", saw " + acquisitionResults.Ms1List.Count);
                        }
                        if (acquisitionResults.Ms2List.Count < NumRequiredMs2Datapoints)
                        {
                            Warn("Calibration failure! Could not find enough MS2 datapoints. Required " + NumRequiredMs2Datapoints + ", saw " + acquisitionResults.Ms2List.Count);
                        }

                        couldNotFindEnoughDatapoints = true;
                        FinishedDataFile(originalUncalibratedFilePath, new List <string> {
                            taskId, "Individual Spectra Files", originalUncalibratedFilePath
                        });
                        break;
                    }

                    Warn("Could not find enough PSMs to calibrate with; opening up tolerances to " +
                         Math.Round(CommonParameters.PrecursorMassTolerance.Value, 2) + " ppm precursor and " +
                         Math.Round(CommonParameters.ProductMassTolerance.Value, 2) + " ppm product");
                }

                if (couldNotFindEnoughDatapoints)
                {
                    spectraFilesAfterCalibration.Add(Path.GetFileNameWithoutExtension(currentRawFileList[spectraFileIndex]));
                    ReportProgress(new ProgressEventArgs(100, "Failed to calibrate!", new List <string> {
                        taskId, "Individual Spectra Files", originalUncalibratedFilenameWithoutExtension
                    }));
                    continue;
                }

                // stats before calibration
                int    prevPsmCount = acquisitionResults.Psms.Count;
                double preCalibrationPrecursorErrorIqr = acquisitionResults.PsmPrecursorIqrPpmError;
                double preCalibrationProductErrorIqr   = acquisitionResults.PsmProductIqrPpmError;

                // generate calibration function and shift data points
                Status("Calibrating...", new List <string> {
                    taskId, "Individual Spectra Files"
                });
                CalibrationEngine engine = new CalibrationEngine(myMsDataFile, acquisitionResults, CommonParameters, FileSpecificParameters, new List <string> {
                    taskId, "Individual Spectra Files", originalUncalibratedFilenameWithoutExtension
                });
                engine.Run();

                //update file
                myMsDataFile = engine.CalibratedDataFile;

                // do another search to evaluate calibration results
                Status("Post-calibration search...", new List <string> {
                    taskId, "Individual Spectra Files"
                });
                acquisitionResults = GetDataAcquisitionResults(myMsDataFile, originalUncalibratedFilePath, variableModifications, fixedModifications, proteinList, taskId, combinedParams, combinedParams.PrecursorMassTolerance, combinedParams.ProductMassTolerance);

                //generate calibration function and shift data points AGAIN because it's fast and contributes new data
                Status("Calibrating...", new List <string> {
                    taskId, "Individual Spectra Files"
                });
                engine = new CalibrationEngine(myMsDataFile, acquisitionResults, CommonParameters, FileSpecificParameters, new List <string> {
                    taskId, "Individual Spectra Files", originalUncalibratedFilenameWithoutExtension
                });
                engine.Run();

                //update file
                myMsDataFile = engine.CalibratedDataFile;

                // write the calibrated mzML file
                MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(myMsDataFile, calibratedFilePath, false);
                myFileManager.DoneWithFile(originalUncalibratedFilePath);

                // stats after calibration
                int    postCalibrationPsmCount          = acquisitionResults.Psms.Count;
                double postCalibrationPrecursorErrorIqr = acquisitionResults.PsmPrecursorIqrPpmError;
                double postCalibrationProductErrorIqr   = acquisitionResults.PsmProductIqrPpmError;

                // did the data improve? (not used for anything yet...)
                bool improvement = ImprovGlobal(preCalibrationPrecursorErrorIqr, preCalibrationProductErrorIqr, prevPsmCount, postCalibrationPsmCount, postCalibrationPrecursorErrorIqr, postCalibrationProductErrorIqr);

                // write toml settings for the calibrated file
                var newTomlFileName = Path.Combine(OutputFolder, originalUncalibratedFilenameWithoutExtension + CalibSuffix + ".toml");

                var fileSpecificParams = new FileSpecificParameters();

                // carry over file-specific parameters from the uncalibrated file to the calibrated one
                if (fileSettingsList[spectraFileIndex] != null)
                {
                    fileSpecificParams = fileSettingsList[spectraFileIndex].Clone();
                }

                //suggest 4 * interquartile range as the ppm tolerance
                fileSpecificParams.PrecursorMassTolerance = new PpmTolerance((4.0 * postCalibrationPrecursorErrorIqr) + Math.Abs(acquisitionResults.PsmPrecursorMedianPpmError));
                fileSpecificParams.ProductMassTolerance   = new PpmTolerance((4.0 * postCalibrationProductErrorIqr) + Math.Abs(acquisitionResults.PsmProductMedianPpmError));

                Toml.WriteFile(fileSpecificParams, newTomlFileName, tomlConfig);

                FinishedWritingFile(newTomlFileName, new List <string> {
                    taskId, "Individual Spectra Files", originalUncalibratedFilenameWithoutExtension
                });

                // finished calibrating this file
                spectraFilesAfterCalibration.Add(Path.GetFileNameWithoutExtension(calibratedFilePath));
                FinishedWritingFile(calibratedFilePath, new List <string> {
                    taskId, "Individual Spectra Files", originalUncalibratedFilenameWithoutExtension
                });
                MyTaskResults.NewSpectra.Add(calibratedFilePath);
                MyTaskResults.NewFileSpecificTomls.Add(newTomlFileName);
                FinishedDataFile(originalUncalibratedFilePath, new List <string> {
                    taskId, "Individual Spectra Files", originalUncalibratedFilePath
                });
                ReportProgress(new ProgressEventArgs(100, "Done!", new List <string> {
                    taskId, "Individual Spectra Files", originalUncalibratedFilenameWithoutExtension
                }));
            }

            // re-write experimental design (if it has been defined) with new calibrated file names
            string assumedPathToExperDesign = Directory.GetParent(currentRawFileList.First()).FullName;

            assumedPathToExperDesign = Path.Combine(assumedPathToExperDesign, GlobalVariables.ExperimentalDesignFileName);

            if (File.Exists(assumedPathToExperDesign))
            {
                WriteNewExperimentalDesignFile(assumedPathToExperDesign, OutputFolder, spectraFilesAfterCalibration);
            }

            // finished calibrating all files for the task
            ReportProgress(new ProgressEventArgs(100, "Done!", new List <string> {
                taskId, "Individual Spectra Files"
            }));

            return(MyTaskResults);
        }
コード例 #2
0
        protected override MyTaskResults RunSpecific(string OutputFolder, List <DbForTask> dbFilenameList, List <string> currentRawFileList, string taskId, FileSpecificParameters[] fileSettingsList)
        {
            // load modifications
            Status("Loading modifications...", new List <string> {
                taskId
            });
            List <ModificationWithMass> variableModifications = GlobalVariables.AllModsKnown.OfType <ModificationWithMass>().Where(b => CommonParameters.ListOfModsVariable.Contains((b.modificationType, b.id))).ToList();
            List <ModificationWithMass> fixedModifications    = GlobalVariables.AllModsKnown.OfType <ModificationWithMass>().Where(b => CommonParameters.ListOfModsFixed.Contains((b.modificationType, b.id))).ToList();
            List <string> localizeableModificationTypes       = GlobalVariables.AllModTypesKnown.ToList();

            // what types of fragment ions to search for
            List <ProductType> ionTypes = new List <ProductType>();

            if (CommonParameters.BIons)
            {
                ionTypes.Add(ProductType.BnoB1ions);
            }
            if (CommonParameters.YIons)
            {
                ionTypes.Add(ProductType.Y);
            }
            if (CommonParameters.ZdotIons)
            {
                ionTypes.Add(ProductType.Zdot);
            }
            if (CommonParameters.CIons)
            {
                ionTypes.Add(ProductType.C);
            }

            // load proteins
            List <Protein> proteinList = LoadProteins(taskId, dbFilenameList, true, DecoyType.Reverse, localizeableModificationTypes, CommonParameters);

            // write prose settings
            ProseCreatedWhileRunning.Append("The following calibration settings were used: ");
            ProseCreatedWhileRunning.Append("protease = " + CommonParameters.DigestionParams.Protease + "; ");
            ProseCreatedWhileRunning.Append("maximum missed cleavages = " + CommonParameters.DigestionParams.MaxMissedCleavages + "; ");
            ProseCreatedWhileRunning.Append("minimum peptide length = " + CommonParameters.DigestionParams.MinPeptideLength + "; ");
            ProseCreatedWhileRunning.Append(CommonParameters.DigestionParams.MaxPeptideLength == int.MaxValue ?
                                            "maximum peptide length = unspecified; " :
                                            "maximum peptide length = " + CommonParameters.DigestionParams.MaxPeptideLength + "; ");
            ProseCreatedWhileRunning.Append("initiator methionine behavior = " + CommonParameters.DigestionParams.InitiatorMethionineBehavior + "; ");
            ProseCreatedWhileRunning.Append("fixed modifications = " + string.Join(", ", fixedModifications.Select(m => m.id)) + "; ");
            ProseCreatedWhileRunning.Append("variable modifications = " + string.Join(", ", variableModifications.Select(m => m.id)) + "; ");
            ProseCreatedWhileRunning.Append("max mods per peptide = " + CommonParameters.DigestionParams.MaxModsForPeptide + "; ");
            ProseCreatedWhileRunning.Append("max modification isoforms = " + CommonParameters.DigestionParams.MaxModificationIsoforms + "; ");
            ProseCreatedWhileRunning.Append("precursor mass tolerance = " + CommonParameters.PrecursorMassTolerance + "; ");
            ProseCreatedWhileRunning.Append("product mass tolerance = " + CommonParameters.ProductMassTolerance + ". ");
            ProseCreatedWhileRunning.Append("The combined search database contained " + proteinList.Count(p => !p.IsDecoy) + " non-decoy protein entries including " + proteinList.Count(p => p.IsContaminant) + " contaminant sequences. ");

            // start the calibration task
            Status("Calibrating...", new List <string> {
                taskId
            });
            MyTaskResults = new MyTaskResults(this)
            {
                NewSpectra           = new List <string>(),
                NewFileSpecificTomls = new List <string>()
            };

            object lock1 = new object();

            var myFileManager = new MyFileManager(true);

            for (int spectraFileIndex = 0; spectraFileIndex < currentRawFileList.Count; spectraFileIndex++)
            {
                if (GlobalVariables.StopLoops)
                {
                    break;
                }

                // get filename stuff
                var    originalUncalibratedFilePath = currentRawFileList[spectraFileIndex];
                var    originalUncalibratedFilenameWithoutExtension = Path.GetFileNameWithoutExtension(originalUncalibratedFilePath);
                string calibratedFilePath = Path.Combine(OutputFolder, originalUncalibratedFilenameWithoutExtension + CalibSuffix + ".mzML");

                // mark the file as in-progress
                StartingDataFile(originalUncalibratedFilePath, new List <string> {
                    taskId, "Individual Spectra Files", originalUncalibratedFilePath
                });

                CommonParameters combinedParams = SetAllFileSpecificCommonParams(CommonParameters, fileSettingsList[spectraFileIndex]);

                MsDataFile myMsDataFile;

                // load the file
                Status("Loading spectra file...", new List <string> {
                    taskId, "Individual Spectra Files"
                });
                lock (lock1)
                {
                    myMsDataFile = myFileManager.LoadFile(originalUncalibratedFilePath, CommonParameters.TopNpeaks, CommonParameters.MinRatio, CommonParameters.TrimMs1Peaks, CommonParameters.TrimMsMsPeaks, CommonParameters);
                }

                // get datapoints to fit calibration function to
                Status("Acquiring calibration data points...", new List <string> {
                    taskId, "Individual Spectra Files"
                });
                DataPointAquisitionResults acquisitionResults = null;

                for (int i = 1; i <= 5; i++)
                {
                    acquisitionResults = GetDataAcquisitionResults(myMsDataFile, originalUncalibratedFilePath, variableModifications, fixedModifications, proteinList, taskId, combinedParams, combinedParams.PrecursorMassTolerance, combinedParams.ProductMassTolerance);

                    // enough data points to calibrate?
                    if (acquisitionResults.Psms.Count >= NumRequiredPsms && acquisitionResults.Ms1List.Count > NumRequiredMs1Datapoints && acquisitionResults.Ms2List.Count > NumRequiredMs2Datapoints)
                    {
                        break;
                    }

                    if (i == 1) // failed round 1
                    {
                        CommonParameters.PrecursorMassTolerance = new PpmTolerance(20);
                        CommonParameters.ProductMassTolerance   = new PpmTolerance(50);
                    }
                    else if (i == 2) // failed round 2
                    {
                        CommonParameters.PrecursorMassTolerance = new PpmTolerance(30);
                        CommonParameters.ProductMassTolerance   = new PpmTolerance(100);
                    }
                    else if (i == 3) // failed round 3
                    {
                        CommonParameters.PrecursorMassTolerance = new PpmTolerance(40);
                        CommonParameters.ProductMassTolerance   = new PpmTolerance(150);
                    }
                    else // failed round 4
                    {
                        if (acquisitionResults.Psms.Count < NumRequiredPsms)
                        {
                            Warn("Calibration failure! Could not find enough high-quality PSMs. Required " + NumRequiredPsms + ", saw " + acquisitionResults.Psms.Count);
                        }
                        if (acquisitionResults.Ms1List.Count < NumRequiredMs1Datapoints)
                        {
                            Warn("Calibration failure! Could not find enough MS1 datapoints. Required " + NumRequiredMs1Datapoints + ", saw " + acquisitionResults.Ms1List.Count);
                        }
                        if (acquisitionResults.Ms2List.Count < NumRequiredMs2Datapoints)
                        {
                            Warn("Calibration failure! Could not find enough MS2 datapoints. Required " + NumRequiredMs2Datapoints + ", saw " + acquisitionResults.Ms2List.Count);
                        }
                        FinishedDataFile(originalUncalibratedFilePath, new List <string> {
                            taskId, "Individual Spectra Files", originalUncalibratedFilePath
                        });
                        return(MyTaskResults);
                    }

                    Warn("Could not find enough PSMs to calibrate with; opening up tolerances to " +
                         Math.Round(CommonParameters.PrecursorMassTolerance.Value, 2) + " ppm precursor and " +
                         Math.Round(CommonParameters.ProductMassTolerance.Value, 2) + " ppm product");
                }

                // stats before calibration
                int    prevPsmCount = acquisitionResults.Psms.Count;
                double preCalibrationPrecursorErrorIqr = acquisitionResults.PsmPrecursorIqrPpmError;
                double preCalibrationProductErrorIqr   = acquisitionResults.PsmProductIqrPpmError;

                // generate calibration function and shift data points
                Status("Calibrating...", new List <string> {
                    taskId, "Individual Spectra Files"
                });
                new CalibrationEngine(myMsDataFile, acquisitionResults, CommonParameters, new List <string> {
                    taskId, "Individual Spectra Files", originalUncalibratedFilenameWithoutExtension
                }).Run();

                // do another search to evaluate calibration results
                Status("Post-calibration search...", new List <string> {
                    taskId, "Individual Spectra Files"
                });
                acquisitionResults = GetDataAcquisitionResults(myMsDataFile, originalUncalibratedFilePath, variableModifications, fixedModifications, proteinList, taskId, combinedParams, combinedParams.PrecursorMassTolerance, combinedParams.ProductMassTolerance);

                // stats after calibration
                int    postCalibrationPsmCount          = acquisitionResults.Psms.Count;
                double postCalibrationPrecursorErrorIqr = acquisitionResults.PsmPrecursorIqrPpmError;
                double postCalibrationProductErrorIqr   = acquisitionResults.PsmProductIqrPpmError;

                // did the data improve? (not used for anything yet...)
                bool improvement = ImprovGlobal(preCalibrationPrecursorErrorIqr, preCalibrationProductErrorIqr, prevPsmCount, postCalibrationPsmCount, postCalibrationPrecursorErrorIqr, postCalibrationProductErrorIqr);

                // write toml settings for the calibrated file
                var newTomlFileName = Path.Combine(OutputFolder, originalUncalibratedFilenameWithoutExtension + CalibSuffix + ".toml");

                var fileSpecificParams = new FileSpecificParameters();

                // carry over file-specific parameters from the uncalibrated file to the calibrated one
                if (fileSettingsList[spectraFileIndex] != null)
                {
                    fileSpecificParams = fileSettingsList[spectraFileIndex].Clone();
                }

                // don't write over ppm tolerances if they've been specified by the user already in the file-specific settings
                // otherwise, suggest 4 * interquartile range as the ppm tolerance
                if (fileSpecificParams.PrecursorMassTolerance == null)
                {
                    fileSpecificParams.PrecursorMassTolerance = new PpmTolerance((4.0 * postCalibrationPrecursorErrorIqr) + Math.Abs(acquisitionResults.PsmPrecursorMedianPpmError));
                }
                if (fileSpecificParams.ProductMassTolerance == null)
                {
                    fileSpecificParams.ProductMassTolerance = new PpmTolerance((4.0 * postCalibrationProductErrorIqr) + Math.Abs(acquisitionResults.PsmProductMedianPpmError));
                }

                Toml.WriteFile(fileSpecificParams, newTomlFileName, tomlConfig);

                FinishedWritingFile(newTomlFileName, new List <string> {
                    taskId, "Individual Spectra Files", originalUncalibratedFilenameWithoutExtension
                });

                // write the calibrated mzML file
                MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(myMsDataFile, calibratedFilePath, false);
                myFileManager.DoneWithFile(originalUncalibratedFilePath);

                // finished calibrating this file
                FinishedWritingFile(calibratedFilePath, new List <string> {
                    taskId, "Individual Spectra Files", originalUncalibratedFilenameWithoutExtension
                });
                MyTaskResults.NewSpectra.Add(calibratedFilePath);
                MyTaskResults.NewFileSpecificTomls.Add(newTomlFileName);
                FinishedDataFile(originalUncalibratedFilePath, new List <string> {
                    taskId, "Individual Spectra Files", originalUncalibratedFilePath
                });
                ReportProgress(new ProgressEventArgs(100, "Done!", new List <string> {
                    taskId, "Individual Spectra Files", originalUncalibratedFilenameWithoutExtension
                }));
            }

            // re-write experimental design (if it has been defined) with new calibrated file names
            string assumedPathToExperDesign = Directory.GetParent(currentRawFileList.First()).FullName;

            assumedPathToExperDesign = Path.Combine(assumedPathToExperDesign, GlobalVariables.ExperimentalDesignFileName);
            List <string> newExperimentalDesignOutput = new List <string>();

            if (File.Exists(assumedPathToExperDesign))
            {
                var lines = File.ReadAllLines(assumedPathToExperDesign);

                for (int i = 0; i < lines.Length; i++)
                {
                    // header of experimental design file
                    if (i == 0)
                    {
                        newExperimentalDesignOutput.Add(lines[i]);
                    }
                    else
                    {
                        var    split   = lines[i].Split('\t');
                        string newline = Path.GetFileNameWithoutExtension(split[0]) + CalibSuffix + "\t";
                        for (int j = 1; j < split.Length; j++)
                        {
                            newline += split[j] + "\t";
                        }

                        newExperimentalDesignOutput.Add(newline);
                    }
                }
            }

            File.WriteAllLines(Path.Combine(OutputFolder, GlobalVariables.ExperimentalDesignFileName), newExperimentalDesignOutput);

            // finished calibrating all files for the task
            ReportProgress(new ProgressEventArgs(100, "Done!", new List <string> {
                taskId, "Individual Spectra Files"
            }));

            return(MyTaskResults);
        }