#include "command.hpp"
#include "nameassignment.hpp"
-#include "globaldata.hpp"
#include "rabundvector.hpp"
#include "sabundvector.hpp"
#include "listvector.hpp"
public:
ClusterDoturCommand(string);
ClusterDoturCommand();
- ~ClusterDoturCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+ ~ClusterDoturCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "cluster.classic"; }
+ string getCommandCategory() { return "Clustering"; }
+ string getHelpString();
+ string getCitation() { return "Schloss PD, Handelsman J (2005). Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501-6. \nhttp://www.mothur.org/wiki/Cluster.classic"; }
+ string getDescription() { return "cluster your sequences into OTUs using DOTUR’s method"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
- bool abort, hard;
+ bool abort, hard, sim;
string method, fileroot, tag, outputDir, phylipfile, namefile;
double cutoff;
int precision, length;
void printData(string label);
vector<string> outputNames;
- map<string, vector<string> > outputTypes;
};
#endif