#include "mothur.h"
#include "command.hpp"
-#include "globaldata.hpp"
-
-
class SeqSummaryCommand : public Command {
public:
+ SeqSummaryCommand(string);
SeqSummaryCommand();
- ~SeqSummaryCommand();
- int execute();
+ ~SeqSummaryCommand(){}
+ vector<string> setParameters();
+ string getCommandName() { return "summary.seqs"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getHelpString();
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
- GlobalData* globaldata;
+ bool abort;
+ string fastafile, outputDir, namefile;
+ int processors;
+ vector<string> outputNames;
+ map<string, int> nameMap;
+
+ struct linePair {
+ unsigned long int start;
+ unsigned long int end;
+ linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
+ };
+
+ vector<linePair*> lines;
+ vector<int> processIDS;
+
+ int createProcessesCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, string);
+ int driverCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, string, linePair*);
+
+ #ifdef USE_MPI
+ int MPICreateSummary(int, int, vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, MPI_File&, MPI_File&, vector<unsigned long int>&);
+ #endif
+
};