sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / venncommand.h

diff --git a/venncommand.h b/venncommand.h
index 3671350072afff05cf0816e66ce649182b00d258..98a59d404099dcb32052e07e93644be9f01e2869 100644 (file)
--- a/venncommand.h
+++ b/venncommand.h
@@ -11,47 +11,50 @@
  
 #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 getOutputPattern(string);   
+       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, sharedOtus;
        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