private static void ShowSyntax(string errorMessage = "")
{
Console.WriteLine();
if (!string.IsNullOrWhiteSpace(errorMessage))
{
ConsoleMsgUtils.ShowErrorCustom("Error: " + errorMessage, false);
Console.WriteLine();
}
var exeName = Path.GetFileName(ProcessFilesOrDirectoriesBase.GetAppPath());
ConsoleWriteWrapped("This program implements a protein parsimony algorithm for grouping proteins with similar peptides.");
Console.WriteLine();
Console.WriteLine("Program syntax #1:");
Console.WriteLine(exeName + " InputFilePath.txt [OutputFilePath]");
Console.WriteLine();
ConsoleWriteWrapped("The input file is a tab delimited text file with columns Protein and Peptide " +
"(column order does not matter; extra columns are ignored)");
Console.WriteLine();
ConsoleWriteWrapped("If the output file path is not defined, it will be created in the same location " +
"as the input file, but with '_parsimony' added to the filename");
Console.WriteLine();
Console.WriteLine("Program syntax #2:");
Console.WriteLine(exeName + " SQLiteDatabase.db3 [TableName]");
Console.WriteLine();
ConsoleWriteWrapped("If the input is a SQLite database file (extension .db, .db3, .sqlite, or\a.sqlite3), " +
"proteins and peptides will be read from the specified table, or\afrom " +
"T_Row_Metadata if TableName is not provided. The table must have columns " +
"Protein and Peptide. Results will be written to tables " +
Runner.PARSIMONY_GROUPING_TABLE + " and " + Runner.PARSIMONY_GROUP_MEMBERS_TABLE);
Console.WriteLine();
Console.WriteLine("Program written by Josh Aldrich for the Department of Energy (PNNL, Richland, WA)");
Console.WriteLine("Version: " + ProcessFilesOrDirectoriesBase.GetAppVersion(PROGRAM_DATE));
Console.WriteLine();
Console.WriteLine("E-mail: [email protected]");
Console.WriteLine("Website: https://github.com/PNNL-Comp-Mass-Spec/ or https://panomics.pnnl.gov/ or https://www.pnnl.gov/integrative-omics or ");
Console.WriteLine(" https://github.com/PNNL-Comp-Mass-Spec");
}
private static string GetAppVersion()
{
return(ProcessFilesOrDirectoriesBase.GetAppVersion(PROGRAM_DATE));
}