class HClusterCommand : public Command {
public:
- HClusterCommand(string);
+ HClusterCommand(string);
+ HClusterCommand();
~HClusterCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
ListVector oldList;
ReadCluster* read;
- bool abort, sorted, print_start;
+ bool abort, sorted, print_start, hard;
string method, fileroot, tag, distfile, format, phylipfile, columnfile, namefile, sort, showabund, timing, outputDir;
double cutoff;
int precision, length;
ofstream sabundFile, rabundFile, listFile;
time_t start;
unsigned long loops;
+ vector<string> outputNames;
+ map<string, vector<string> > outputTypes;
void printData(string label);
};