*
*/
-#include <iostream>
-#include <fstream>
-#include <map>
#include "command.hpp"
#include "rabundvector.hpp"
#include "sharedlistvector.h"
#include "inputdata.h"
#include "groupmap.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
/* The parselist() command:
public:
ParseListCommand();
~ParseListCommand();
- int execute();
+ int execute();
+ void help() {}
private:
GlobalData* globaldata;
GroupMap* groupMap;
InputData* input;
- ReadMatrix* read;
+ ReadOTUFile* read;
map<string, ofstream*> filehandles;
map<string, SharedListVector*> groupOfLists;
SharedListVector* list;
map<string, string>::iterator it;
map<string, SharedListVector*>::iterator it2;
map<string, ofstream*>::iterator it3;
- void parse(int);
+ void parse(int, SharedListVector*);
+ void process(SharedListVector*);
string fileroot;
};