#include "mothur.h"
#include "command.hpp"
#include "chimera.h"
+#include "chimeracheckrdp.h"
/***********************************************************/
class ChimeraCheckCommand : public Command {
public:
ChimeraCheckCommand(string);
- ~ChimeraCheckCommand();
- int execute();
- void help();
+ ChimeraCheckCommand();
+ ~ChimeraCheckCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "chimera.check"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getHelpString();
+ string getCitation() { return "CHIMERA_CHECK version 2.7 written by Niels Larsen (http://wdcm.nig.ac.jp/RDP/docs/chimera_doc.html) \nhttp://www.mothur.org/wiki/Chimera.check"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
-
private:
struct linePair {
unsigned long int start;
- int numSeqs;
- linePair(unsigned long int i, int j) : start(i), numSeqs(j) {}
+ unsigned long int end;
+ linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
};
+
vector<int> processIDS; //processid
vector<linePair*> lines;
int createProcesses(string, string);
#ifdef USE_MPI
- int driverMPI(int, int, MPI_File&, MPI_File&, vector<long>&);
+ int driverMPI(int, int, MPI_File&, MPI_File&, vector<unsigned long int>&);
#endif
bool abort, svg;
vector<string> fastaFileNames;
vector<string> nameFileNames;
vector<string> outputNames;
-
};
/***********************************************************/