#include "tree.h"
#include "treemap.h"
#include "sharedutilities.h"
-
-class GlobalData;
class ConcensusCommand : public Command {
public:
ConcensusCommand(string);
ConcensusCommand();
- ~ConcensusCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+ ~ConcensusCommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "concensus"; }
+ string getCommandCategory() { return "Hidden"; }
+ string getHelpString();
+ string getCitation() { return "no citation"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
private:
- GlobalData* globaldata;
SharedUtil* util;
vector<Tree*> t;
Tree* consensusTree;
ofstream out, out2;
int numNodes, numLeaves, count; //count is the next available spot in the tree vector
vector<string> outputNames;
- map<string, vector<string> > outputTypes;
int getSets();
int getSubgroupRating(vector<string>);