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 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
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 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);
}
}
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);
}
/// <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)
{
// Returns True if no problems; otherwise, returns false
var lstValidParameters = new List <string> {
"Mode", "Runtime", "Threads", "UseTiered", "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);
}
// Could query commandLineParser to see if various parameters are present
//if (commandLineParser.NonSwitchParameterCount > 0)
//{
// mFileName = commandLineParser.RetrieveNonSwitchParameter(0);
//}
var modeValue = 0;
if (!GetParamInt(commandLineParser, "Mode", ref modeValue))
{
return(false);
}
try
{
if (modeValue > 0)
{
mProcessingMode = (eProcessingMode)(modeValue - 1);
}
}
catch (Exception ex)
{
ShowErrorMessage("Invalid value for /Mode; should be /Mode:1 or /Mode:2 or /Mode:3 or /Mode:4", ex);
}
if (!GetParamInt(commandLineParser, "Runtime", ref mRuntimeSeconds))
{
return(false);
}
if (commandLineParser.IsParameterPresent("Threads"))
{
if (!GetParamInt(commandLineParser, "Threads", ref mThreadCount))
{
return(false);
}
}
else
{
mThreadCount = GetCoreCount();
}
mUseTieredRuntimes = commandLineParser.IsParameterPresent("UseTiered");
mPreviewMode = commandLineParser.IsParameterPresent("Preview");
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);
}