private static void ParseCommandLineParameters(clsParseCommandLine commandLineParser) { mExtractScanFilters = commandLineParser.IsParameterPresent("GetFilters"); if (commandLineParser.NonSwitchParameterCount > 0) { mSourceFilePath = commandLineParser.RetrieveNonSwitchParameter(0); } mCentroid = commandLineParser.IsParameterPresent("centroid"); mTestSumming = commandLineParser.IsParameterPresent("sum"); mStartScan = 0; mEndScan = 0; if (commandLineParser.RetrieveValueForParameter("Start", out var startScan)) { if (int.TryParse(startScan, out var value)) { mStartScan = value; } } if (commandLineParser.RetrieveValueForParameter("End", out var endScan)) { if (int.TryParse(endScan, out var value)) { mEndScan = value; } } if (commandLineParser.RetrieveValueForParameter("ScanInfo", out var scanInfoInterval)) { if (int.TryParse(scanInfoInterval, out var value)) { mScanInfoInterval = value; } } if (commandLineParser.IsParameterPresent("NoScanData")) { mLoadScanData = false; } if (commandLineParser.IsParameterPresent("NoScanEvents")) { mGetScanEvents = false; } if (commandLineParser.IsParameterPresent("NoCE")) { mLoadCollisionEnergies = false; } mOnlyLoadMSLevelInfo = commandLineParser.IsParameterPresent("MSLevelOnly"); mTestScanFilters = commandLineParser.IsParameterPresent("TestFilters"); mTraceMode = commandLineParser.IsParameterPresent("Trace"); }
private static bool SetOptionsUsingCommandLineParameters(clsParseCommandLine objParseCommandLine) { // Returns True if no problems; otherwise, returns false var lstValidParameters = new List <string> { "F", "L" }; try { // Make sure no invalid parameters are present if (objParseCommandLine.InvalidParametersPresent(lstValidParameters)) { var badArguments = new List <string>(); foreach (var item in objParseCommandLine.InvalidParameters(lstValidParameters)) { badArguments.Add("/" + item); } ShowErrorMessage("Invalid commmand line parameters", badArguments); return(false); } // Query objParseCommandLine to see if various parameters are present if (objParseCommandLine.NonSwitchParameterCount > 0) { mDanteFilePath = objParseCommandLine.RetrieveNonSwitchParameter(0); } if (!ParseParameter(objParseCommandLine, "F", "a session file path", ref mDanteFilePath)) { return(false); } if (!ParseParameter(objParseCommandLine, "L", "a log file path", ref mLogFilePath)) { return(false); } return(true); } catch (Exception ex) { ShowErrorMessage("Error parsing the command line parameters: " + Environment.NewLine + ex.Message); } return(false); }
private static bool SetOptionsUsingCommandLineParameters(clsParseCommandLine commandLineParser) { // Returns True if no problems; otherwise, returns false var validParameters = new List <string>() { "I" }; try { // Make sure no invalid parameters are present if (commandLineParser.InvalidParametersPresent(validParameters)) { ShowErrorMessage("Invalid command line parameters", (from item in commandLineParser.InvalidParameters(validParameters) select("/" + item)).ToList()); return(false); } // Query commandLineParser to see if various parameters are present if (commandLineParser.RetrieveValueForParameter("I", out var inputFilePath)) { mInputFilePath = inputFilePath; } else if (commandLineParser.NonSwitchParameterCount > 0) { // Treat the first non-switch parameter as the input file mInputFilePath = commandLineParser.RetrieveNonSwitchParameter(0); } return(true); } catch (Exception ex) { ShowErrorMessage("Error parsing the command line parameters: " + Environment.NewLine + ex.Message); } return(false); }
private static bool SetOptionsUsingCommandLineParameters(clsParseCommandLine commandLineParser) { // Returns True if no problems; otherwise, returns false var validParameters = new List <string> { "I", "M", "O", "N", "C", "Mage", "Append", "DartID", "S", "A", "R" }; try { // Make sure no invalid parameters are present if (commandLineParser.InvalidParametersPresent(validParameters)) { ShowErrorMessage("Invalid command line parameters", (from item in commandLineParser.InvalidParameters(validParameters) select "/" + item).ToList()); return(false); } // Query commandLineParser to see if various parameters are present if (commandLineParser.RetrieveValueForParameter("I", out var inputFile)) { mInputFilePath = inputFile; } else if (commandLineParser.NonSwitchParameterCount > 0) { mInputFilePath = commandLineParser.RetrieveNonSwitchParameter(0); } if (commandLineParser.RetrieveValueForParameter("M", out var masicResultsDir)) { mMASICResultsDirectoryPath = masicResultsDir; } if (commandLineParser.RetrieveValueForParameter("O", out var outputDirectory)) { mOutputDirectoryPath = outputDirectory; } if (commandLineParser.RetrieveValueForParameter("N", out var scanNumColumnIndex)) { if (int.TryParse(scanNumColumnIndex, out var value)) { mScanNumberColumn = value; } } if (commandLineParser.IsParameterPresent("C")) { mSeparateByCollisionMode = true; } if (commandLineParser.IsParameterPresent("Mage")) { mMageResults = true; } if (commandLineParser.IsParameterPresent("Append")) { mMergeWildcardResults = true; } if (commandLineParser.IsParameterPresent("DartID")) { mCreateDartIdInputFile = true; } if (commandLineParser.RetrieveValueForParameter("S", out var maxLevelsToRecurse)) { mRecurseDirectories = true; if (int.TryParse(maxLevelsToRecurse, out var levels)) { mRecurseDirectoriesMaxLevels = levels; } } if (commandLineParser.RetrieveValueForParameter("A", out var alternatePath)) { mOutputDirectoryAlternatePath = alternatePath; } if (commandLineParser.IsParameterPresent("R")) { mRecreateDirectoryHierarchyInAlternatePath = true; } return(true); } catch (Exception ex) { ShowErrorMessage("Error parsing the command line parameters", ex); } return(false); }
private static bool SetOptionsUsingCommandLineParameters(clsParseCommandLine commandLineParse) { // Returns True if no problems; otherwise, returns false var lstValidParameters = new List <string> { "I", "P", "Package", "V", "Version", "Preview", "Apply", "Rollback", "S", "Verbose" }; try { // Make sure no invalid parameters are present if (commandLineParse.InvalidParametersPresent(lstValidParameters)) { var badArguments = new List <string>(); foreach (var item in commandLineParse.InvalidParameters(lstValidParameters)) { badArguments.Add("/" + item); } ShowErrorMessage("Invalid command line parameters", badArguments); return(false); } // Query commandLineParse to see if various parameters are present if (commandLineParse.NonSwitchParameterCount > 0) { mSearchDirectoryPath = commandLineParse.RetrieveNonSwitchParameter(0); } if (commandLineParse.RetrieveValueForParameter("I", out var paramValue)) { mSearchDirectoryPath = string.Copy(paramValue); } if (commandLineParse.RetrieveValueForParameter("Package", out paramValue)) { mUpdateOptions.NuGetPackageName = paramValue; } else if (commandLineParse.RetrieveValueForParameter("P", out paramValue)) { mUpdateOptions.NuGetPackageName = paramValue; } if (commandLineParse.RetrieveValueForParameter("Version", out paramValue)) { mUpdateOptions.NuGetPackageVersion = paramValue; } else if (commandLineParse.RetrieveValueForParameter("V", out paramValue)) { mUpdateOptions.NuGetPackageVersion = paramValue; } if (commandLineParse.IsParameterPresent("Apply")) { mUpdateOptions.Preview = false; } if (commandLineParse.IsParameterPresent("Preview")) { mUpdateOptions.Preview = true; } if (commandLineParse.IsParameterPresent("Rollback")) { mUpdateOptions.Rollback = true; } if (commandLineParse.IsParameterPresent("S")) { mRecurse = true; } if (commandLineParse.IsParameterPresent("Verbose")) { mVerboseLogging = true; } return(true); } catch (Exception ex) { ShowErrorMessage("Error parsing the command line parameters", ex); } return(false); }
private static bool SetOptionsUsingCommandLineParameters(clsParseCommandLine commandLineParser) { // Returns True if no problems; otherwise, returns false var lstValidParameters = new List <string> { "I", "O", "F", "S", "Preview" }; try { // Make sure no invalid parameters are present if (commandLineParser.InvalidParametersPresent(lstValidParameters)) { var badArguments = new List <string>(); foreach (var item in commandLineParser.InvalidParameters(lstValidParameters)) { badArguments.Add("/" + item); } ShowErrorMessage("Invalid command line parameters", badArguments); return(false); } // Query commandLineParser to see if various parameters are present if (commandLineParser.NonSwitchParameterCount > 0) { mFileMask = commandLineParser.RetrieveNonSwitchParameter(0); } if (!ParseParameter(commandLineParser, "I", "a file mask specification", ref mFileMask)) { return(false); } if (!ParseParameter(commandLineParser, "O", "an output file path", ref mOutputFilePath)) { return(false); } if (commandLineParser.IsParameterPresent("F")) { mFullPathsInResults = true; } if (commandLineParser.IsParameterPresent("Preview")) { mPreviewMode = true; } if (commandLineParser.IsParameterPresent("S")) { mRecurse = true; } return(true); } catch (Exception ex) { ShowErrorMessage("Error parsing the command line parameters: " + ex.Message, ex); } return(false); }
private static bool SetOptionsUsingCommandLineParameters(clsParseCommandLine commandLineParser) { // Returns True if no problems; otherwise, returns false // /I:PeptideInputFilePath /R: ProteinInputFilePath /O:OutputDirectoryPath /P:ParameterFilePath var validParameters = new List <string>() { "I", "O", "R", "P", "G", "H", "M", "K", "Debug", "KeepDB" }; try { // Make sure no invalid parameters are present if (commandLineParser.InvalidParametersPresent(validParameters)) { ShowErrorMessage("Invalid command line parameters", (from item in commandLineParser.InvalidParameters(validParameters) select("/" + item)).ToList()); return(false); } // Query commandLineParser to see if various parameters are present if (commandLineParser.RetrieveValueForParameter("I", out var inputFilePath)) { mPeptideInputFilePath = inputFilePath; } else if (commandLineParser.NonSwitchParameterCount > 0) { mPeptideInputFilePath = commandLineParser.RetrieveNonSwitchParameter(0); } if (commandLineParser.RetrieveValueForParameter("O", out var outputDirectoryPath)) { mOutputDirectoryPath = outputDirectoryPath; } if (commandLineParser.RetrieveValueForParameter("R", out var proteinFile)) { mProteinInputFilePath = proteinFile; } if (commandLineParser.RetrieveValueForParameter("P", out var parameterFile)) { mParameterFilePath = parameterFile; } if (commandLineParser.RetrieveValueForParameter("H", out _)) { mOutputProteinSequence = false; } mIgnoreILDifferences = commandLineParser.IsParameterPresent("G"); mSaveProteinToPeptideMappingFile = commandLineParser.IsParameterPresent("M"); mSkipCoverageComputationSteps = commandLineParser.IsParameterPresent("K"); mDebugMode = commandLineParser.IsParameterPresent("Debug"); mKeepDB = commandLineParser.IsParameterPresent("KeepDB"); return(true); } catch (Exception ex) { ShowErrorMessage("Error parsing the command line parameters: " + Environment.NewLine + ex.Message); } return(false); }
private static bool SetOptionsUsingCommandLineParameters(clsParseCommandLine objParseCommandLine) { // Returns True if no problems; otherwise, returns false var lstValidParameters = new List <string> { "I", "O", "AltOutput", "Folders", "S", "NoWild", "Ext" }; try { // Make sure no invalid parameters are present if (objParseCommandLine.InvalidParametersPresent(lstValidParameters)) { var badArguments = new List <string>(); foreach (var item in objParseCommandLine.InvalidParameters(lstValidParameters)) { badArguments.Add("/" + item); } ShowErrorMessage("Invalid command line parameters", badArguments); return(false); } // Query objParseCommandLine to see if various parameters are present if (objParseCommandLine.NonSwitchParameterCount > 0) { mInputFileOrFolderPath = objParseCommandLine.RetrieveNonSwitchParameter(0); } if (objParseCommandLine.NonSwitchParameterCount > 1) { mOutputFileOrFolderPath = objParseCommandLine.RetrieveNonSwitchParameter(1); } if (objParseCommandLine.RetrieveValueForParameter("I", out var paramValue)) { mInputFileOrFolderPath = string.Copy(paramValue); } if (objParseCommandLine.RetrieveValueForParameter("O", out paramValue)) { mOutputFileOrFolderPath = string.Copy(paramValue); } if (objParseCommandLine.RetrieveValueForParameter("AltOutput", out paramValue)) { mOutputFolderAlternatePath = string.Copy(paramValue); } if (objParseCommandLine.IsParameterPresent("Folders")) { mProcessFolders = true; } mRecurse = objParseCommandLine.IsParameterPresent("S"); if (mRecurse && objParseCommandLine.RetrieveValueForParameter("S", out paramValue)) { if (int.TryParse(paramValue, out var recurseDepth)) { mRecurseDepth = recurseDepth; } } mAssumeNoWildcards = objParseCommandLine.IsParameterPresent("NoWild"); if (mRecurse && objParseCommandLine.RetrieveValueForParameter("Ext", out paramValue)) { var extensions = paramValue.Split(','); if (extensions.Length > 0) { mKnownExtensions.Clear(); mKnownExtensions.AddRange(extensions); } } return(true); } catch (Exception ex) { ShowErrorMessage("Error parsing the command line parameters: " + Environment.NewLine + ex.Message, ex); } return(false); }
private static bool SetOptionsUsingCommandLineParameters(clsParseCommandLine CommandLineParser) { // Returns True if no problems; otherwise, returns false // /I:PeptideInputFilePath /R: ProteinInputFilePath /O:OutputDirectoryPath /P:ParameterFilePath string value = string.Empty; var validParameters = new List <string>() { "I", "O", "R", "P", "F", "N", "G", "H", "K", "A", "L", "LogDir", "LogFolder", "VerboseLog" }; int intValue; try { // Make sure no invalid parameters are present if (CommandLineParser.InvalidParametersPresent(validParameters)) { ShowErrorMessage("Invalid command line parameters", (from item in CommandLineParser.InvalidParameters(validParameters) select("/" + item)).ToList()); return(false); } else { // Query commandLineParser to see if various parameters are present if (CommandLineParser.RetrieveValueForParameter("I", out value)) { mPeptideInputFilePath = value; } else if (CommandLineParser.NonSwitchParameterCount > 0) { mPeptideInputFilePath = CommandLineParser.RetrieveNonSwitchParameter(0); } if (CommandLineParser.RetrieveValueForParameter("O", out value)) { mOutputDirectoryPath = value; } if (CommandLineParser.RetrieveValueForParameter("R", out value)) { mProteinInputFilePath = value; } if (CommandLineParser.RetrieveValueForParameter("P", out value)) { mParameterFilePath = value; } if (CommandLineParser.RetrieveValueForParameter("F", out value)) { if (int.TryParse(value, out intValue)) { try { mInputFileFormatCode = (clsPeptideToProteinMapEngine.ePeptideInputFileFormatConstants)intValue; } catch (Exception ex) { // Conversion failed; leave mInputFileFormatCode unchanged } } } if (CommandLineParser.RetrieveValueForParameter("N", out value)) { mInspectParameterFilePath = value; } if (CommandLineParser.RetrieveValueForParameter("G", out value)) { mIgnoreILDifferences = true; } if (CommandLineParser.RetrieveValueForParameter("H", out value)) { mOutputProteinSequence = false; } if (CommandLineParser.RetrieveValueForParameter("K", out value)) { mSkipCoverageComputationSteps = true; } if (CommandLineParser.RetrieveValueForParameter("A", out value)) { mSaveSourceDataPlusProteinsFile = true; } if (CommandLineParser.RetrieveValueForParameter("L", out value)) { mLogMessagesToFile = true; if (!string.IsNullOrEmpty(value)) { mLogFilePath = value; } } if (CommandLineParser.RetrieveValueForParameter("LogDir", out value)) { mLogMessagesToFile = true; if (!string.IsNullOrEmpty(value)) { mLogDirectoryPath = value; } } if (CommandLineParser.RetrieveValueForParameter("LogFolder", out value)) { mLogMessagesToFile = true; if (!string.IsNullOrEmpty(value)) { mLogDirectoryPath = value; } } if (CommandLineParser.RetrieveValueForParameter("VerboseLog", out value)) { mVerboseLogging = true; } return(true); } } catch (Exception ex) { ShowErrorMessage("Error parsing the command line parameters: " + Environment.NewLine + ex.Message); } return(false); }
public static void Main() { mScanInfoInterval = 1; mLoadMethods = true; mLoadScanData = true; mGetScanEvents = true; mLoadCollisionEnergies = true; mOnlyLoadMSLevelInfo = false; var commandLineParser = new clsParseCommandLine(); commandLineParser.ParseCommandLine(); if (commandLineParser.NeedToShowHelp) { ShowProgramHelp(); return; } if (Path.DirectorySeparatorChar == '/') { mSourceFilePath = DEFAULT_FILE_PATH.Replace('\\', '/'); } else { mSourceFilePath = DEFAULT_FILE_PATH; } ParseCommandLineParameters(commandLineParser); if (mExtractScanFilters) { var workingDirectory = "."; if (commandLineParser.NonSwitchParameterCount > 0) { workingDirectory = commandLineParser.RetrieveNonSwitchParameter(0); } ExtractScanFilters(workingDirectory); System.Threading.Thread.Sleep(1500); return; } var sourceFile = new FileInfo(mSourceFilePath); if (!sourceFile.Exists) { Console.WriteLine("File not found: " + sourceFile.FullName); System.Threading.Thread.Sleep(1500); return; } if (mTestScanFilters) { TestScanFilterParsing(); } TestReader(sourceFile.FullName, mCentroid, mTestSumming, mStartScan, mEndScan); if (mCentroid) { // Also process the file with centroiding off TestReader(sourceFile.FullName, false, mTestSumming, mStartScan, mEndScan); } if (mGetScanEvents) { TestGetAllScanEvents(sourceFile.FullName); } Console.WriteLine("Done"); System.Threading.Thread.Sleep(150); }
//private static void SaveTestPlots() //{ // // var plotter = new clsTICandBPIPlotter("modMain", true); // var testChart = new LiveCharts.WinForms.CartesianChart(); // testChart.Series = new SeriesCollection // { // new LineSeries // { // Title = "Series 1", // Values = new ChartValues<double> {4, 6, 5, 2, 7} // }, // new LineSeries // { // Title = "Series 2", // Values = new ChartValues<double> {6, 7, 3, 4, 6}, // PointGeometry = null // }, // //new LineSeries // //{ // // Title = "Series 2", // // Values = new ChartValues<double> {5, 2, 8, 3}, // // PointGeometry = DefaultGeometries.Square, // // PointGeometrySize = 15 // //} // }; // Console.WriteLine("Update XAxis"); // testChart.AxisX.Add(new Axis // { // Title = "Month", // Labels = new[] { "Jan", "Feb", "Mar", "Apr", "May" } // }); // testChart.AxisY.Add(new Axis // { // Title = "Sales", // LabelFormatter = value => value.ToString("C") // }); // Console.WriteLine("Add legend"); // testChart.LegendLocation = LegendLocation.Right; // ////modifying the series collection will animate and update the chart // //testChart.Series.Add(new LineSeries // //{ // // Values = new ChartValues<double> { 5, 3, 2, 4, 5 }, // // LineSmoothness = 0, //straight lines, 1 really smooth lines // // PointGeometry = Geometry.Parse("m 25 70.36218 20 -28 -20 22 -8 -6 z"), // // PointGeometrySize = 50, // // PointForeground = System.Windows.Media.Brushes.Gray // //}); // //modifying any series values will also animate and update the chart // // testChart.Series[2].Values.Add(5d); // //Viewbox viewBox = WrapChart(testChart, 1400, 700); // // testChart.Model.Updater.Run(false, true); // Console.WriteLine("Call AddTitleToChart"); // var panel = AddTitleToChart(testChart, "My title"); // Console.WriteLine("Update chart"); // testChart.Update(false, true); // Console.WriteLine("Render as bitmap"); // using (Bitmap printImage = new Bitmap(panel.Width, panel.Height)) // { // panel.DrawToBitmap(printImage, new Rectangle(0, 0, printImage.Width, printImage.Height)); // var fileName = "TestExport" + DateTime.Now.ToString("yyyy-MM-dd_hh_mm_ss") + ".png"; // printImage.Save(fileName, ImageFormat.Png); // } // //var plotTest = new frmPlot(); // //plotTest.Show(); // Console.WriteLine("Saved"); //} //public static TableLayoutPanel AddTitleToChart(Control chart, string title) //{ // Console.WriteLine("Add label"); // Label label = new Label(); // label.AutoSize = true; // label.Dock = System.Windows.Forms.DockStyle.Fill; // label.Font = new Font("Arial", 12); // label.Location = new System.Drawing.Point(3, 0); // label.Name = "label1"; // label.Size = new System.Drawing.Size(1063, 55); // label.TabIndex = 0; // label.Text = title; // label.TextAlign = System.Drawing.ContentAlignment.MiddleCenter; // label.BackColor = chart.BackColor; // chart.Dock = System.Windows.Forms.DockStyle.Fill; // Console.WriteLine("Create TableLayoutPanel"); // TableLayoutPanel tableLayoutPanel = new TableLayoutPanel(); // tableLayoutPanel.AutoSize = true; // tableLayoutPanel.AutoSizeMode = System.Windows.Forms.AutoSizeMode.GrowAndShrink; // tableLayoutPanel.BackColor = System.Drawing.Color.White; // tableLayoutPanel.ColumnCount = 1; // tableLayoutPanel.ColumnStyles.Add(new System.Windows.Forms.ColumnStyle(System.Windows.Forms.SizeType.Absolute, 1069F)); // Console.WriteLine("Add label to TableLayoutPanel"); // tableLayoutPanel.Controls.Add(label, 0, 0); // Console.WriteLine("Add chart to TableLayoutPanel"); // tableLayoutPanel.Controls.Add(chart, 0, 1); // Console.WriteLine("Update TableLayoutPanel DockStyle"); // tableLayoutPanel.Dock = System.Windows.Forms.DockStyle.Fill; // tableLayoutPanel.Location = new System.Drawing.Point(0, 0); // tableLayoutPanel.Name = "tableLayoutPanel1"; // Console.WriteLine("Set Rowcount= 2"); // tableLayoutPanel.RowCount = 2; // tableLayoutPanel.RowStyles.Add(new System.Windows.Forms.RowStyle()); // tableLayoutPanel.RowStyles.Add(new System.Windows.Forms.RowStyle()); // Console.WriteLine("Define size"); // tableLayoutPanel.Size = new System.Drawing.Size(1069, 662); // Console.WriteLine("Set tab index"); // tableLayoutPanel.TabIndex = 2; // return (tableLayoutPanel); //} //public Viewbox viewBox WrapChart(CartesianChart testChart, Grid grid, int width, int height) //{ // testChart.grid.Width = width; // testChart.grid.Height = height; // viewbox.Child = chart.grid; // viewbox.Width = width; // viewbox.Height = height; // viewbox.Measure(new System.Windows.Size(width, height)); // viewbox.Arrange(new Rect(0, 0, width, height)); // viewbox.UpdateLayout(); //} private static bool SetOptionsUsingCommandLineParameters(clsParseCommandLine parser) { // Returns True if no problems; otherwise, returns false var lstValidParameters = new List <string> { "I", "O", "P", "S", "IE", "L", "C", "M", "H", "QZ", "NoTIC", "LC", "LCDiv", "LCGrad", "CC", "QS", "ScanStart", "ScanEnd", "DatasetID", "DI", "DST", "SS", "CF", "R", "Z", "PostToDMS", "Debug", "Python", "PythonPlot" }; try { // Make sure no invalid parameters are present if (parser.InvalidParametersPresent(lstValidParameters)) { ShowErrorMessage("Invalid commmand line parameters", (from item in parser.InvalidParameters(lstValidParameters) select "/" + item).ToList()); return(false); } int value; // Query parser to see if various parameters are present if (parser.RetrieveValueForParameter("I", out var strValue)) { mInputDataFilePath = strValue; } else if (parser.NonSwitchParameterCount > 0) { // Treat the first non-switch parameter as the input file mInputDataFilePath = parser.RetrieveNonSwitchParameter(0); } if (parser.RetrieveValueForParameter("O", out strValue)) { mOutputFolderName = strValue; } if (parser.RetrieveValueForParameter("P", out strValue)) { mParameterFilePath = strValue; } if (parser.RetrieveValueForParameter("S", out strValue)) { mRecurseFolders = true; if (int.TryParse(strValue, out value)) { mRecurseFoldersMaxLevels = value; } } if (parser.RetrieveValueForParameter("IE", out strValue)) { mIgnoreErrorsWhenRecursing = true; } if (parser.RetrieveValueForParameter("L", out strValue)) { mLogFilePath = strValue; } if (parser.IsParameterPresent("C")) { mCheckFileIntegrity = true; } if (parser.RetrieveValueForParameter("M", out strValue)) { if (int.TryParse(strValue, out value)) { mMaximumTextFileLinesToCheck = value; } } if (parser.IsParameterPresent("H")) { mComputeFileHashes = true; } if (parser.IsParameterPresent("QZ")) { mZipFileCheckAllData = false; } if (parser.IsParameterPresent("NoTIC")) { mSaveTICandBPIPlots = false; } if (parser.RetrieveValueForParameter("LC", out strValue)) { mSaveLCMS2DPlots = true; if (int.TryParse(strValue, out value)) { mLCMS2DMaxPointsToPlot = value; } } if (parser.RetrieveValueForParameter("LCDiv", out strValue)) { if (int.TryParse(strValue, out value)) { mLCMS2DOverviewPlotDivisor = value; } } if (parser.IsParameterPresent("LCGrad")) { mTestLCMSGradientColorSchemes = true; } if (parser.IsParameterPresent("CC")) { mCheckCentroidingStatus = true; } if (parser.RetrieveValueForParameter("ScanStart", out strValue)) { if (int.TryParse(strValue, out value)) { mScanStart = value; } } if (parser.RetrieveValueForParameter("ScanEnd", out strValue)) { if (int.TryParse(strValue, out value)) { mScanEnd = value; } } if (parser.IsParameterPresent("Debug")) { mShowDebugInfo = true; } if (parser.IsParameterPresent("QS")) { mComputeOverallQualityScores = true; } if (parser.RetrieveValueForParameter("DatasetID", out strValue)) { if (!int.TryParse(strValue, out mDatasetID)) { ShowErrorMessage("DatasetID is not an integer"); return(false); } } if (parser.IsParameterPresent("DI")) { mCreateDatasetInfoFile = true; } if (parser.IsParameterPresent("SS")) { mCreateScanStatsFile = true; } if (parser.RetrieveValueForParameter("DST", out strValue)) { mUpdateDatasetStatsTextFile = true; if (!string.IsNullOrEmpty(strValue)) { mDatasetStatsTextFileName = strValue; } } if (parser.IsParameterPresent("CF")) { mUseCacheFiles = true; } if (parser.IsParameterPresent("R")) { mReprocessingExistingFiles = true; } if (parser.IsParameterPresent("Z")) { mReprocessIfCachedSizeIsZero = true; } if (parser.IsParameterPresent("PostToDMS")) { mPostResultsToDMS = true; } if (parser.IsParameterPresent("PythonPlot") || parser.IsParameterPresent("Python")) { mPlotWithPython = true; } return(true); } catch (Exception ex) { ShowErrorMessage("Error parsing the command line parameters: " + Environment.NewLine + ex.Message); return(false); } }
/// <summary> /// Set options using command line parameters /// </summary> /// <param name="commandLineParser"></param> /// <returns>True if no problems; otherwise, returns false</returns> private static bool SetOptionsUsingCommandLineParameters(clsParseCommandLine commandLineParser) { var validParameters = new List <string> { "Local", "Preview", "Trace", "LogDB", "FS" }; try { // Make sure no invalid parameters are present if (commandLineParser.InvalidParametersPresent(validParameters)) { var badArguments = new List <string>(); foreach (var item in commandLineParser.InvalidParameters(validParameters)) { badArguments.Add("/" + item); } ShowErrorMessage("Invalid command line parameters", badArguments); return(false); } // Query commandLineParser to see if various parameters are present if (commandLineParser.NonSwitchParameterCount > 0) { mMTSServer = commandLineParser.RetrieveNonSwitchParameter(0); } if (commandLineParser.IsParameterPresent("Local")) { mLocalServerMode = true; } if (commandLineParser.IsParameterPresent("Preview")) { mPreviewMode = true; } if (commandLineParser.IsParameterPresent("Trace")) { mTraceMode = true; } if (commandLineParser.RetrieveValueForParameter("LogDB", out var strValue)) { if (string.IsNullOrWhiteSpace(strValue)) { ShowErrorMessage("/LogDB does not have a value; not overriding the logging connection string"); } else { mLogDBConnectionString = strValue; } } if (commandLineParser.RetrieveValueForParameter("FS", out strValue)) { if (string.IsNullOrWhiteSpace(strValue)) { ShowErrorMessage("/FS does not have a value; not overriding the minimum free space"); } else { if (!int.TryParse(strValue, out mMinimumCacheFreeSpaceGB)) { ShowErrorMessage("Error converting " + strValue + " to an integer for parameter /FS"); } } } return(true); } catch (Exception ex) { ShowErrorMessage("Error parsing the command line parameters: " + Environment.NewLine + ex.Message); } return(false); }
private static bool SetOptionsUsingCommandLineParameters(clsParseCommandLine commandLineParser, SplitterOptions options) { // Returns True if no problems; otherwise, returns false var validParameters = new List <string> { "I", "N", "MB", "O", "P", "S", "A", "R", "L" }; try { // Make sure no invalid parameters are present if (commandLineParser.InvalidParametersPresent(validParameters)) { ConsoleMsgUtils.ShowErrors("Invalid command line parameters", (from item in commandLineParser.InvalidParameters(validParameters) select("/" + item)).ToList()); return(false); } // Query commandLineParser to see if various parameters are present if (commandLineParser.RetrieveValueForParameter("I", out var inputFilePath)) { mInputFilePath = inputFilePath; } else if (commandLineParser.NonSwitchParameterCount > 0) { mInputFilePath = commandLineParser.RetrieveNonSwitchParameter(0); } if (commandLineParser.RetrieveValueForParameter("N", out var splitCount)) { if (int.TryParse(splitCount, out var value)) { options.SplitCount = value; } else { ConsoleMsgUtils.ShowError( "Error parsing number from the /N parameter; " + "for example, use /N:{0} to specify the file be split into {0} parts", SplitterOptions.DEFAULT_SPLIT_COUNT); options.SplitCount = SplitterOptions.DEFAULT_SPLIT_COUNT; } } if (commandLineParser.RetrieveValueForParameter("MB", out var targetSizeMB)) { options.UseTargetFileSize = true; if (int.TryParse(targetSizeMB, out var value)) { options.TargetFastaFileSizeMB = value; } else { ConsoleMsgUtils.ShowError( "Error parsing number from the /MB parameter; " + "for example, use /MB:{0} to specify the file be split into files that are each {0} MB in size", SplitterOptions.DEFAULT_TARGET_FILE_SIZE_MB); options.TargetFastaFileSizeMB = SplitterOptions.DEFAULT_TARGET_FILE_SIZE_MB; } } if (commandLineParser.RetrieveValueForParameter("O", out var outputDirectory)) { mOutputDirectoryName = outputDirectory; } if (commandLineParser.RetrieveValueForParameter("P", out var parameterFile)) { mParameterFilePath = parameterFile; } if (commandLineParser.RetrieveValueForParameter("S", out var recurseSubdirectories)) { mRecurseDirectories = true; if (!int.TryParse(recurseSubdirectories, out mMaxLevelsToRecurse)) { mMaxLevelsToRecurse = 0; } } if (commandLineParser.RetrieveValueForParameter("A", out var alternateOutputDirectory)) { mOutputDirectoryAlternatePath = alternateOutputDirectory; } if (commandLineParser.IsParameterPresent("R")) { mRecreateDirectoryHierarchyInAlternatePath = true; } if (commandLineParser.IsParameterPresent("L")) { mLogMessagesToFile = true; } return(true); } catch (Exception ex) { ConsoleMsgUtils.ShowError("Error parsing the command line parameters", ex); return(false); } }
private static bool SetOptionsUsingCommandLineParameters(clsParseCommandLine objParseCommandLine) { // Returns True if no problems; otherwise, returns false var lstValidParameters = new List <string> { "I", "O", "PK", "NoP", "NoG", "Def", "Definition", "Com", "Comm", "Comment" }; try { // Make sure no invalid parameters are present if (objParseCommandLine.InvalidParametersPresent(lstValidParameters)) { var badArguments = new List <string>(); foreach (var item in objParseCommandLine.InvalidParameters(lstValidParameters)) { badArguments.Add("/" + item); } ShowErrorMessage("Invalid commmand line parameters", badArguments); return(false); } // Query objParseCommandLine to see if various parameters are present if (objParseCommandLine.NonSwitchParameterCount > 0) { mInputFilePath = objParseCommandLine.RetrieveNonSwitchParameter(0); } if (objParseCommandLine.NonSwitchParameterCount > 1) { mOutputFilePath = objParseCommandLine.RetrieveNonSwitchParameter(1); } string paramValue; if (objParseCommandLine.RetrieveValueForParameter("I", out paramValue)) { mInputFilePath = string.Copy(paramValue); } if (objParseCommandLine.RetrieveValueForParameter("O", out paramValue)) { mOutputFilePath = string.Copy(paramValue); } if (objParseCommandLine.RetrieveValueForParameter("PK", out paramValue)) { mPrimaryKeySuffix = string.Copy(paramValue); } if (objParseCommandLine.IsParameterPresent("NoP")) { mOutputOptions.IncludeParentTerms = false; mOutputOptions.IncludeGrandparentTerms = false; } if (objParseCommandLine.IsParameterPresent("NoG")) { mOutputOptions.IncludeGrandparentTerms = false; } if (objParseCommandLine.IsParameterPresent("Def") || objParseCommandLine.IsParameterPresent("Definition")) { mOutputOptions.IncludeDefinition = true; } if (objParseCommandLine.IsParameterPresent("Com") || objParseCommandLine.IsParameterPresent("Comm") || objParseCommandLine.IsParameterPresent("Comment")) { mOutputOptions.IncludeComment = true; } return(true); } catch (Exception ex) { ShowErrorMessage("Error parsing the command line parameters", ex); } return(false); }
/// <summary> /// Set options using command line arguments /// </summary> /// <param name="commandLineParser"></param> /// <returns>True if no problems; otherwise, false</returns> private static bool SetOptionsUsingCommandLineParameters(clsParseCommandLine commandLineParser) { var validParameters = new List <string> { "I", "O", "P", "D", "S", "A", "R", "L", "Log", "SF", "LogDir", "LogFolder", "Q" }; try { // Make sure no invalid parameters are present if (commandLineParser.InvalidParametersPresent(validParameters)) { ShowErrorMessage("Invalid command line parameters", (from item in commandLineParser.InvalidParameters(validParameters) select("/" + item)).ToList()); return(false); } // Query commandLineParser to see if various parameters are present if (commandLineParser.RetrieveValueForParameter("I", out var inputFilePath)) { mInputFilePath = inputFilePath; } else if (commandLineParser.NonSwitchParameterCount > 0) { // Treat the first non-switch parameter as the input file mInputFilePath = commandLineParser.RetrieveNonSwitchParameter(0); } if (commandLineParser.RetrieveValueForParameter("O", out var outputDirectoryPath)) { mOutputDirectoryPath = outputDirectoryPath; } if (commandLineParser.RetrieveValueForParameter("P", out var parameterFilePath)) { mParameterFilePath = parameterFilePath; } if (commandLineParser.RetrieveValueForParameter("D", out var datasetIdOrLookupFile)) { if (int.TryParse(datasetIdOrLookupFile, out var datasetId)) { mDatasetID = datasetId; } else if (!string.IsNullOrWhiteSpace(datasetIdOrLookupFile)) { // Assume the user specified a dataset number lookup file comma, space, or tab delimited delimited file specifying the dataset number for each input file) mDatasetLookupFilePath = datasetIdOrLookupFile; mDatasetID = 0; } } if (commandLineParser.RetrieveValueForParameter("S", out var recursionDepth)) { mRecurseDirectories = true; if (int.TryParse(recursionDepth, out var levelsToRecurse)) { mMaxLevelsToRecurse = levelsToRecurse; } } if (commandLineParser.RetrieveValueForParameter("A", out var alternateOutputDirectory)) { mOutputDirectoryAlternatePath = alternateOutputDirectory; } if (commandLineParser.IsParameterPresent("R")) { mRecreateDirectoryHierarchyInAlternatePath = true; } var logFileName = string.Empty; var logToFile = false; if (commandLineParser.IsParameterPresent("L")) { logToFile = commandLineParser.RetrieveValueForParameter("L", out logFileName); } else if (commandLineParser.IsParameterPresent("Log")) { logToFile = commandLineParser.RetrieveValueForParameter("Log", out logFileName); } if (logToFile) { mLogMessagesToFile = true; if (!string.IsNullOrEmpty(logFileName)) { mLogFilePath = logFileName.Trim('"'); } } if (commandLineParser.RetrieveValueForParameter("SF", out var masicStatusFile)) { mMASICStatusFilename = masicStatusFile; } if (commandLineParser.RetrieveValueForParameter("LogDir", out var logDirectoryPath)) { mLogMessagesToFile = true; if (!string.IsNullOrEmpty(logDirectoryPath)) { mLogDirectoryPath = logDirectoryPath; } } if (commandLineParser.RetrieveValueForParameter("LogFolder", out var logFolderPath)) { mLogMessagesToFile = true; if (!string.IsNullOrEmpty(logFolderPath)) { mLogDirectoryPath = logFolderPath; } } if (commandLineParser.IsParameterPresent("Q")) { mQuietMode = true; } return(true); } catch (Exception ex) { ShowErrorMessage("Error parsing the command line parameters: " + Environment.NewLine + ex.Message); } return(false); }