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