#include "sabundvector.hpp"
#include "listvector.hpp"
#include "cluster.hpp"
-#include "sparsematrix.hpp"
+#include "sparsedistancematrix.h"
+#include "counttable.h"
/* The cluster() command:
The cluster command outputs a .list , .rabund and .sabund files.
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 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();
private:
Cluster* cluster;
- SparseMatrix* matrix;
+ SparseDistanceMatrix* matrix;
ListVector* list;
RAbundVector* rabund;
RAbundVector oldRAbund;
bool abort, hard, sim;
- string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, format, distfile;
+ string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, format, distfile, countfile;
double cutoff;
string showabund, timing;
int precision, length;
void printData(string label);
vector<string> outputNames;
+
+ int createRabund(CountTable*&, ListVector*&, RAbundVector*&);
};
#endif