#include "command.hpp"
#include "sharedordervector.h"
-#include "sharedlistvector.h"
#include "inputdata.h"
-#include "groupmap.h"
#include "collect.h"
#include "display.h"
-#include "readotu.h"
#include "validcalculator.h"
#include "sharedutilities.h"
-class GlobalData;
class CollectSharedCommand : public Command {
public:
CollectSharedCommand(string);
+ CollectSharedCommand();
~CollectSharedCommand();
- int execute();
- void help();
+
+ vector<string> setParameters();
+ string getCommandName() { return "collect.shared"; }
+ string getCommandCategory() { return "OTU-Based Approaches"; }
+ string getOutputFileNameTag(string, string);
+ string getHelpString();
+ string getCitation() { return "Schloss PD, Handelsman J (2006). Introducing SONS, A tool that compares the membership of microbial communities. Appl Environ Microbiol 72: 6773-9. \nhttp://www.mothur.org/wiki/Collect.shared"; }
+ string getDescription() { return "generates collector's curves for calculators, which describe the similarity between communities or their shared richness"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
private:
- GlobalData* globaldata;
- SharedUtil* util;
- GroupMap* groupmap;
- SharedListVector* SharedList;
- ReadOTUFile* read;
SharedOrderVector* order;
InputData* input;
- ValidCalculators* validCalculator;
Collect* cCurve;
vector<Display*> cDisplays;
float freq;
- string format;
bool abort, allLines, all;
set<string> labels; //holds labels to be used
- string label, calc, groups, outputDir;
+ string label, calc, groups, outputDir, sharedfile;
vector<string> Estimators, Groups, outputNames;
-
-
};
#endif