*/
#include "command.hpp"
-#include "globaldata.hpp"
#include "hcluster.h"
#include "rabundvector.hpp"
#include "sabundvector.hpp"
public:
HClusterCommand(string);
HClusterCommand();
- ~HClusterCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+ ~HClusterCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "hcluster"; }
+ string getCommandCategory() { return "Clustering"; }
+
+ string getHelpString();
+ string getOutputPattern(string);
+ string getCitation() { return "Sun Y, Cai Y, Liu L, Yu F, Farrell ML, Mckendree W, Farmerie W (2009). ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences. Nucleic Acids Res 37: e76. \nhttp://www.mothur.org/wiki/Hcluster"; }
+ string getDescription() { return "cluster your sequences into OTUs using a distance matrix"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
private:
- GlobalData* globaldata;
HCluster* cluster;
ListVector* list;
RAbundVector* rabund;
time_t start;
unsigned long loops;
vector<string> outputNames;
- map<string, vector<string> > outputTypes;
void printData(string label);
};