added classify.shared command and random forest files. added count file to pcr.seqs...

[mothur.git] / venncommand.h

diff --git a/venncommand.h b/venncommand.h
index f8151c1bdf0e3a547638639dfbf2aa5ac9f437ed..9f369280fc66e53754da98a4b6252568a7960d90 100644 (file)
--- a/venncommand.h
+++ b/venncommand.h
@@ -11,35 +11,49 @@
  
 #include "command.hpp"
 #include "inputdata.h"
-#include "readmatrix.hpp"
 #include "sharedlistvector.h"
 #include "venn.h"
-
-
-class GlobalData;
-
+#include "validcalculator.h"
 
 class VennCommand : public Command {
 
 public:
+       VennCommand(string);
        VennCommand();
-       ~VennCommand();
-       int execute();
+       ~VennCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "venn";                                        }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getOutputFileNameTag(string, string);
+       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;
-       ReadMatrix* read;
        InputData* input;
        SharedListVector* SharedList;
-       SharedOrderVector* order;
-       OrderVector* ordersingle;
        Venn* venn;
-       string format;
+       vector<Calculator*> vennCalculators;    
+       vector<SharedRAbundVector*> lookup;
+       set< set<int> > combosOfFour;
+       SAbundVector* sabund;
+       int abund, fontsize;
+       
+       bool abort, allLines, nseqs, perm;
+       set<string> labels; //holds labels to be used
+       string format, groups, calc, label, outputDir, sharedfile, listfile, inputfile;
+       vector<string> Estimators, Groups, outputNames;
        
-       void setGroups();
+       set< set<int> > findCombinations(int);
+       int getCombos(set<int>, set< set<int> >&);
+
 
 };
 
 
 
-#endif
\ No newline at end of file
+#endif