1 #ifndef SEQSUMMARYCOMMAND_H
2 #define SEQSUMMARYCOMMAND_H
8 * Created by Pat Schloss on 5/30/09.
9 * Copyright 2009 Patrick D. Schloss. All rights reserved.
14 #include "command.hpp"
16 class SeqSummaryCommand : public Command {
18 SeqSummaryCommand(string);
21 vector<string> getRequiredParameters();
22 vector<string> getValidParameters();
23 vector<string> getRequiredFiles();
24 map<string, vector<string> > getOutputFiles() { return outputTypes; }
30 string fastafile, outputDir, namefile;
32 vector<string> outputNames;
33 map<string, vector<string> > outputTypes;
34 map<string, int> nameMap;
37 unsigned long int start;
38 unsigned long int end;
39 linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
42 vector<linePair*> lines;
43 vector<int> processIDS;
45 int createProcessesCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, string);
46 int driverCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, string, linePair*);
50 int MPICreateSummary(int, int, vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, MPI_File&, MPI_File&, vector<unsigned long int>&);