#include "command.hpp"
#include "inputdata.h"
-#include "readotu.h"
#include "sabundvector.hpp"
-class GlobalData;
-
class GetSAbundCommand : public Command {
public:
+ GetSAbundCommand(string);
GetSAbundCommand();
- ~GetSAbundCommand();
- int execute();
+ ~GetSAbundCommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "get.sabund"; }
+ string getCommandCategory() { return "OTU-Based Approaches"; }
+ string getOutputFileNameTag(string, string);
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Get.sabund"; }
+ string getDescription() { return "creates a sabund file"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
- GlobalData* globaldata;
- string filename, format;
+ string filename, format, inputfile, listfile, rabundfile, outputDir;
ofstream out;
- ReadOTUFile* read;
- OrderVector* order;
- OrderVector* lastOrder;
InputData* input;
SAbundVector* sabund;
+ vector<string> outputNames;
+
+ bool abort, allLines;
+ set<string> labels; //holds labels to be used
+ string label;
+
};
#endif