#include "command.hpp"
#include "inputdata.h"
-#include "readotu.h"
#include "listvector.hpp"
-class GlobalData;
class GetRAbundCommand : public Command {
public:
GetRAbundCommand(string);
GetRAbundCommand();
- ~GetRAbundCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+ ~GetRAbundCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "get.rabund"; }
+ string getCommandCategory() { return "OTU-Based Approaches"; }
+ string getOutputFileNameTag(string, string);
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Get.rabund"; }
+ string getDescription() { return "creates a rabund file"; }
+
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
private:
- GlobalData* globaldata;
- string filename;
+
+ string filename, listfile, sabundfile, inputfile, format, outputDir;
ofstream out;
- ReadOTUFile* read;
InputData* input;
- ListVector* list;
RAbundVector* rabund;
vector<string> outputNames;
- map<string, vector<string> > outputTypes;
bool abort, allLines, sorted;
set<string> labels; //holds labels to be used