/// <summary> /// /// </summary> /// <param name="nonAlignedPairsFile"></param> public string GetFatcatAlignmentsOnLinux(string nonAlignedPairsFile) { if (ProtCidSettings.dirSettings == null) { ProtCidSettings.LoadDirSettings(); } if (ProtCidSettings.alignmentDbConnection == null) { ProtCidSettings.alignmentDbConnection = new DbLib.DbConnect(); ProtCidSettings.alignmentDbConnection.ConnectString = "DRIVER=Firebird/InterBase(r) driver;UID=SYSDBA;" + "PWD=fbmonkeyox;DATABASE=" + ProtCidSettings.dirSettings.alignmentDbPath; } string repChainPairsFileName = "NonAlignRepEntryPairs.txt"; WriteRepChainPairsToFile(nonAlignedPairsFile, repChainPairsFileName); CmdOperations linuxOperator = new CmdOperations(); linuxOperator.CopyWindowsDataToLinux(repChainPairsFileName, exeFatcatDir + repChainPairsFileName); string cmdLineFile = WriteFatcatCommandFile(repChainPairsFileName); linuxOperator.RunPlink(cmdLineFile); string alignFileInLinux = fatcatDir + repChainPairsFileName.Replace(".txt", ".aln"); string alignFileInWindows = Path.Combine(ProtCidSettings.dirSettings.fatcatPath, repChainPairsFileName.Replace(".txt", ".aln")); linuxOperator.CopyLinuxDataToWindows(alignFileInLinux, alignFileInWindows); return(alignFileInWindows); }