#include "command.hpp"
#include "inputdata.h"
-#include "readotu.h"
#include "sharedrabundvector.h"
-class GlobalData;
class GetRelAbundCommand : public Command {
public:
GetRelAbundCommand(string);
GetRelAbundCommand();
- ~GetRelAbundCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+ ~GetRelAbundCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "get.relabund"; }
+ string getCommandCategory() { return "OTU-Based Approaches"; }
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Get.relabund"; }
+ string getDescription() { return "calculates the relative abundance of each OTU in a sample"; }
+
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
- GlobalData* globaldata;
- ReadOTUFile* read;
InputData* input;
vector<SharedRAbundVector*> lookup;
bool abort, allLines, pickedGroups;
set<string> labels; //holds labels to be used
- string groups, label, outputDir, scale;
+ string groups, label, outputDir, scale, sharedfile;
vector<string> Groups, outputNames;
- map<string, vector<string> > outputTypes;
int getRelAbundance(vector<SharedRAbundVector*>&, ofstream&);