#include "command.hpp"
#include "inputdata.h"
#include "listvector.hpp"
-#include "readotu.h"
-
-class GlobalData;
/**********************************************************/
public:
GetListCountCommand(string);
GetListCountCommand();
- ~GetListCountCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+ ~GetListCountCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "get.otulist"; }
+ string getCommandCategory() { return "OTU-Based Approaches"; }
+ string getCitation() { return "http://www.mothur.org/wiki/Get.otulist"; }
+ string getDescription() { return "lists each OTU number and the sequence contained in that OTU"; }
+
+
+ string getHelpString();
+ string getOutputPattern(string);
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
private:
- GlobalData* globaldata;
ListVector* list;
- ReadOTUFile* read;
InputData* input;
bool abort, allLines;
string label, listfile, outputDir, sort;
ofstream out;
vector<string> outputNames;
- map<string, vector<string> > outputTypes;
-
+
void process(ListVector*);
};
/**********************************************************/