1 #ifndef CHIMERACCODECOMMAND_H
2 #define CHIMERACCODECOMMAND_H
5 * chimeraccodecommand.h
8 * Created by westcott on 3/30/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
14 #include "command.hpp"
18 /***********************************************************/
20 class ChimeraCcodeCommand : public Command {
22 ChimeraCcodeCommand(string);
23 ChimeraCcodeCommand();
24 ~ChimeraCcodeCommand();
25 vector<string> getRequiredParameters();
26 vector<string> getValidParameters();
27 vector<string> getRequiredFiles();
28 map<string, vector<string> > getOutputFiles() { return outputTypes; }
35 unsigned long int start;
36 unsigned long int end;
37 linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
39 vector<int> processIDS; //processid
40 vector<linePair*> lines;
42 int driver(linePair*, string, string, string);
43 int createProcesses(string, string, string);
46 int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
50 string fastafile, templatefile, outputDir, maskfile;
51 int processors, window, numwanted, numSeqs, templateSeqsLength;
53 vector<string> fastaFileNames;
54 vector<string> outputNames;
55 map<string, vector<string> > outputTypes;
60 /***********************************************************/