#include "mothur.h"
#include "command.hpp"
-#include "chimera.h"
-
/***********************************************************/
class ChimeraSeqsCommand : public Command {
public:
ChimeraSeqsCommand(string);
+ ChimeraSeqsCommand() {}
~ChimeraSeqsCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map< string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
private:
-
- bool abort;
- string method, fastafile, templatefile, consfile, quanfile, maskfile;
- bool filter, correction;
- int processors, midpoint, averageLeft, averageRight, window, iters, increment, numwanted;
- Chimera* chimera;
-
-
+ vector<string> outputNames;
+ map< string, vector<string> > outputTypes;
+
};
/***********************************************************/