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);
20 ~SeqSummaryCommand(){}
22 vector<string> setParameters();
23 string getCommandName() { return "summary.seqs"; }
24 string getCommandCategory() { return "Sequence Processing"; }
25 string getHelpString();
26 string getCitation() { return "http://www.mothur.org/wiki/Summary.seqs"; }
29 void help() { m->mothurOut(getHelpString()); }
32 string fastafile, outputDir, namefile;
34 vector<string> outputNames;
35 map<string, int> nameMap;
38 unsigned long int start;
39 unsigned long int end;
40 linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
43 vector<linePair*> lines;
44 vector<int> processIDS;
46 int createProcessesCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, string);
47 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>&);