public static void DoJob()
{
String fastaFile = "C:\\Users\\LavalleeLab\\Documents\\JoshTemp\\RealTimeMS\\TestData\\uniprot_SwissProt_Human_1_11_2017.fasta";
String outputFile = "C:\\Users\\LavalleeLab\\Documents\\JoshTemp\\RealTimeMS\\TestData\\";
DecoyConcacenatedDatabaseGenerator.GenerateConcacenatedDecoyFasta(fastaFile);
}
private static void ConstructDecoyFasta()
{
if (!GlobalVar.useDecoyFastaComputedFile)
{
log.Debug("Generating decoy database for comet search validation");
InputFileOrganizer.DecoyFasta = DecoyConcacenatedDatabaseGenerator.GenerateConcacenatedDecoyFasta(InputFileOrganizer.FASTA_FILE, InputFileOrganizer.preExperimentFilesFolder);
log.Debug("Concacenated decoy database generated.");
}
}
private static void SimulationWithDecoyParamsSetUp()
{
GlobalVar.isSimulationForFeatureExtraction = true;
String decoyConcatDB = DecoyConcacenatedDatabaseGenerator.GenerateConcacenatedDecoyFasta(InputFileOrganizer.FASTA_FILE, InputFileOrganizer.OutputFolderOfTheRun);
InputFileOrganizer.ExclusionDBFasta = decoyConcatDB; //sets the in-program databse to one that contains decoy protein - for feature generation only
InputFileOrganizer.DecoyFasta = decoyConcatDB;
GlobalVar.useDecoyFastaComputedFile = true;
GlobalVar.useIDXComputedFile = false;
GlobalVar.useChainsawComputedFile = false;
GlobalVar.usePepXMLComputedFile = false;
GlobalVar.useRTCalcComputedFile = false;
//InputFileOrganizer.RTCalcResult = "C:\\Users\\LavalleeLab\\Documents\\JoshTemp\\RealTimeMS\\TestData\\PreComputedFiles\\tempOutputPeptideList_rtOutput_240min.txt";
}