*
*/
+/* The bin.seqs command outputs a .fasta file for each distance you specify appending the OTU number to each name. */
#include "command.hpp"
#include "inputdata.h"
#include "listvector.hpp"
-#include "readmatrix.hpp"
+#include "readotu.h"
#include "fastamap.h"
+#include "groupmap.h"
class GlobalData;
private:
GlobalData* globaldata;
ListVector* list;
- ReadMatrix* read;
+ ReadOTUFile* read;
InputData* input;
FastaMap* fasta;
- string filename, fastafile, namesfile;
+ GroupMap* groupMap;
+ string filename, fastafile, namesfile, groupfile;
ofstream out;
ifstream in, inNames;
void readNamesFile();
+ int process(ListVector*, int);
};
#endif