#include "command.hpp"
#include "inputdata.h"
-#include "readotu.h"
#include "sharedlistvector.h"
#include "venn.h"
#include "validcalculator.h"
-
-class GlobalData;
-
-
class VennCommand : public Command {
public:
VennCommand(string);
- ~VennCommand();
- int execute();
- void help();
+ VennCommand();
+ ~VennCommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "venn"; }
+ string getCommandCategory() { return "OTU-Based Approaches"; }
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Venn"; }
+ string getDescription() { return "generates a Venn diagram from data provided in a shared file"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
- GlobalData* globaldata;
- ReadOTUFile* read;
InputData* input;
SharedListVector* SharedList;
Venn* venn;
vector<Calculator*> vennCalculators;
- ValidCalculators* validCalculator;
vector<SharedRAbundVector*> lookup;
+ set< set<int> > combosOfFour;
SAbundVector* sabund;
- int abund;
+ int abund, fontsize;
- OptionParser* parser;
- map<string, string> parameters;
- map<string, string>::iterator it;
- bool abort, allLines;
- set<int> lines; //hold lines to be used
+ bool abort, allLines, nseqs, perm;
set<string> labels; //holds labels to be used
- string format, groups, calc, line, label;
- vector<string> Estimators, Groups;
+ string format, groups, calc, label, outputDir, sharedfile, listfile, inputfile;
+ vector<string> Estimators, Groups, outputNames;
+
+ set< set<int> > findCombinations(int);
+ int getCombos(set<int>, set< set<int> >&);
};
-#endif
\ No newline at end of file
+#endif