*/
#include "command.hpp"
-#include "globaldata.hpp"
#include "rabundvector.hpp"
#include "sabundvector.hpp"
#include "listvector.hpp"
#include "sparsematrix.hpp"
/* The cluster() command:
- The cluster command can only be executed after a successful read.phylip or read.column command.
The cluster command outputs a .list , .rabund and .sabund files.
The cluster command parameter options are method, cuttoff and precision. No parameters are required.
The cluster command should be in the following format: cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision).
The cluster() command outputs three files *.list, *.rabund, and *.sabund. */
-class GlobalData;
-
class ClusterCommand : public Command {
public:
- ClusterCommand(string);
+ ClusterCommand(string);
+ ClusterCommand();
~ClusterCommand();
- int execute();
- void help();
+
+ vector<string> setParameters();
+ string getCommandName() { return "cluster"; }
+ string getCommandCategory() { return "Clustering"; }
+ string getHelpString();
+ string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol. \nhttp://www.mothur.org/wiki/Cluster"; }
+ string getDescription() { return "cluster your sequences into OTUs using a distance matrix"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
- GlobalData* globaldata;
Cluster* cluster;
SparseMatrix* matrix;
ListVector* list;
RAbundVector oldRAbund;
ListVector oldList;
- bool abort;
+ bool abort, hard, sim;
- string method, fileroot, tag;
+ string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, format, distfile;
double cutoff;
+ string showabund, timing;
int precision, length;
ofstream sabundFile, rabundFile, listFile;
+
+ bool print_start;
+ time_t start;
+ unsigned long loops;
void printData(string label);
+ vector<string> outputNames;
};
#endif