*/
#include "command.hpp"
-#include "globaldata.hpp"
#include "hcluster.h"
#include "rabundvector.hpp"
#include "sabundvector.hpp"
class HClusterCommand : public Command {
public:
- HClusterCommand(string);
- ~HClusterCommand();
- int execute();
- void help();
+ HClusterCommand(string);
+ HClusterCommand();
+ ~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;
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;
void printData(string label);
};