*
*/
-#include <Carbon/Carbon.h>
-#include <iostream>
-#include <fstream>
#include "command.hpp"
-#include "readmatrix.hpp"
+#include "readotu.h"
#include "inputdata.h"
#include "groupmap.h"
#include "sharedcommand.h"
class ReadOtuCommand : public Command {
public:
- ReadOtuCommand();
+ ReadOtuCommand(string);
~ReadOtuCommand();
int execute();
+ void help();
private:
GlobalData* globaldata;
- ReadMatrix* read;
+ //ReadOTUFile* read;
InputData* input;
Command* shared;
Command* parselist;
GroupMap* groupMap;
- string filename;
+ string filename, listfile, orderfile, sharedfile, line, label, groupfile, sabundfile, rabundfile, format;
+
+ bool abort, allLines;
+ set<int> lines; //hold lines to be used
+ set<string> labels; //holds labels to be used
+
};
-#endif
\ No newline at end of file
+#endif