The cluster() command outputs three files *.list, *.rabund, and *.sabund. */
-class GlobalData;
-
class ClusterCommand : public Command {
public:
- ClusterCommand(string);
+ ClusterCommand(string);
~ClusterCommand();
int execute();
void help();
RAbundVector* rabund;
RAbundVector oldRAbund;
ListVector oldList;
- OptionParser* parser;
- map<string, string> parameters;
- map<string, string>::iterator it;
- bool abort;
- string method, fileroot, tag;
+ bool abort, hard;
+
+ string method, fileroot, tag, outputDir;
double cutoff;
+ string showabund, timing;
int precision, length;
ofstream sabundFile, rabundFile, listFile;
+
+ bool print_start;
+ time_t start;
+ unsigned long loops;
void printData(string label);
+ vector<string> outputNames;
};
#endif