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();
33 linePair(long int i, int j) : start(i), numSeqs(j) {}
35 vector<int> processIDS; //processid
36 vector<linePair*> lines;
38 int driver(linePair*, string, string, string);
39 int createProcesses(string, string, string);
42 int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<long>&);
45 bool abort, filter, MPIWroteAccnos;
46 string fastafile, templatefile, outputDir, maskfile;
47 int processors, window, numwanted, numSeqs, templateSeqsLength;
53 /***********************************************************/