#include "inputdata.h"
#include "rarefact.h"
#include "display.h"
-#include "readotu.h"
#include "validcalculator.h"
-
-class GlobalData;
-
class RareFactCommand : public Command {
public:
- RareFactCommand(string);
- ~RareFactCommand();
- int execute();
- void help();
+ RareFactCommand(string);
+ RareFactCommand();
+ ~RareFactCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "rarefaction.single"; }
+ string getCommandCategory() { return "OTU-Based Approaches"; }
+ string getHelpString();
+ string getCitation() { return "Magurran AE (2004). Measuring biological diversity. Blackwell Pub.: Malden, Ma. \nhttp://www.mothur.org/wiki/Rarefaction.single"; }
+ string getDescription() { return "generate intra-sample rarefaction curves using a re-sampling without replacement approach"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
- GlobalData* globaldata;
+
vector<Display*> rDisplays;
- ReadOTUFile* read;
OrderVector* order;
InputData* input;
- ValidCalculators* validCalculator;
Rarefact* rCurve;
- int freq, nIters, abund;
-
- bool abort, allLines;
+ int nIters, abund, processors;
+ float freq;
+
+ bool abort, allLines, groupMode;
set<string> labels; //holds labels to be used
- string label, calc;
+ string label, calc, sharedfile, listfile, rabundfile, sabundfile, format, inputfile;
vector<string> Estimators;
- vector<string> inputFileNames;
+ vector<string> inputFileNames, outputNames;
vector<string> groups;
+ string outputDir;
vector<string> parseSharedFile(string);
-
-
+ vector<string> createGroupFile(vector<string>&, map<int, string>);
};
#endif