added diffs and percent parameters to cluster.fragments command

[mothur.git] / venncommand.h

diff --git a/venncommand.h b/venncommand.h
index d91aaef1c7e47185862cf1a681976a31c47ebb75..29beeadc32f422f8b053e1da86f483032e496e8d 100644 (file)
--- a/venncommand.h
+++ b/venncommand.h
@@ -11,7 +11,7 @@
  
 #include "command.hpp"
 #include "inputdata.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
 #include "sharedlistvector.h"
 #include "venn.h"
 #include "validcalculator.h"
@@ -23,27 +23,41 @@ class GlobalData;
 class VennCommand : public Command {
 
 public:
+       VennCommand(string);
        VennCommand();
        ~VennCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
+       void help();
        
 private:
        GlobalData* globaldata;
-       ReadMatrix* read;
+       ReadOTUFile* read;
        InputData* input;
        SharedListVector* SharedList;
-       SharedOrderVector* order;
-       OrderVector* ordersingle;
        Venn* venn;
-       string format;
        vector<Calculator*> vennCalculators;    
        ValidCalculators* validCalculator;
+       vector<SharedRAbundVector*> lookup;
+       set< set<int> > combosOfFour;
+       SAbundVector* sabund;
        int abund;
        
-       void setGroups();
+       bool abort, allLines, nseqs, perm;
+       set<string> labels; //holds labels to be used
+       string format, groups, calc, label, outputDir;
+       vector<string> Estimators, Groups, outputNames;
+       map<string, vector<string> > outputTypes;
+       
+       set< set<int> > findCombinations(int);
+       int getCombos(set<int>, set< set<int> >&);
+
 
 };
 
 
 
-#endif
\ No newline at end of file
+#endif