*/
#include "command.hpp"
-#include "globaldata.hpp"
#include "rabundvector.hpp"
#include "sabundvector.hpp"
#include "listvector.hpp"
#include "cluster.hpp"
-#include "sparsematrix.hpp"
+#include "sparsedistancematrix.h"
+#include "counttable.h"
/* 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();
+ ClusterCommand(string);
+ ClusterCommand();
~ClusterCommand();
- int execute();
+
+ vector<string> setParameters();
+ string getCommandName() { return "cluster"; }
+ string getCommandCategory() { return "Clustering"; }
+
+ string getHelpString();
+ string getOutputPattern(string);
+ 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 77:3219.\nSchloss 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"; }
+ 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;
+ SparseDistanceMatrix* matrix;
ListVector* list;
RAbundVector* rabund;
RAbundVector oldRAbund;
ListVector oldList;
-
- string method, fileroot, tag;
+
+ bool abort, hard, sim;
+
+ string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, format, distfile, countfile;
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;
+
+ int createRabund(CountTable*&, ListVector*&, RAbundVector*&);
};
#endif