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();
30 unsigned long int start;
31 unsigned long int end;
32 linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
34 vector<int> processIDS; //processid
35 vector<linePair*> lines;
37 int driver(linePair*, string, string, string);
38 int createProcesses(string, string, string);
41 int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
45 string fastafile, templatefile, outputDir, maskfile;
46 int processors, window, numwanted, numSeqs, templateSeqsLength;
48 vector<string> fastaFileNames;
49 vector<string> outputNames;
54 /***********************************************************/