#include "mothur.h"
#include "command.hpp"
-#include "globaldata.hpp"
-#include "readfasta.h"
-#include "readnexus.h"
-#include "readclustal.h"
-#include "readseqsphylip.h"
-
-using namespace std;
class SeqSummaryCommand : public Command {
public:
- SeqSummaryCommand();
+ SeqSummaryCommand(string);
~SeqSummaryCommand();
int execute();
+ void help();
private:
- int numSeqs;
- GlobalData* globaldata;
- ReadSeqs* readSeqs;
- SequenceDB* db;
+ bool abort;
+ string fastafile, outputDir;
+ int processors;
+
+ struct linePair {
+ int start;
+ int num;
+ linePair(long int i, long int j) : start(i), num(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>&);
+ #endif
+
+
};
#endif