reworked amova / homova / anosim

[mothur.git] / amovacommand.h

diff --git a/amovacommand.h b/amovacommand.h
index d9fe1e6fe7e941c89ed65ffafce0f0ad2cc72c61..51a420064fc0e560cebb291035b1d9245febce5c 100644 (file)
--- a/amovacommand.h
+++ b/amovacommand.h
@@ -11,12 +11,9 @@
  */
 
 #include "command.hpp"
-#include "inputdata.h"
-#include "sharedrabundvector.h"
-#include "validcalculator.h"
-#include "readphylipvector.h"
 
-class GlobalData;
+//class GlobalData;
+class GroupMap;
 
 class AmovaCommand : public Command {
        
@@ -39,7 +36,6 @@ private:
 
        
        bool abort;
-       GlobalData* globaldata;
        map<string, vector<string> > outputTypes;
        vector<string> outputNames;
 
@@ -48,23 +44,6 @@ private:
        vector< vector<double> > distanceMatrix;
        int iters;
        double experimentwiseAlpha;
-       
-//     struct linePair {
-//             int start;
-//             int num;
-//             linePair(int i, int j) : start(i), num(j) {}
-//     };
-//     vector<linePair> lines;
-//
-//     vector< vector<string> > namesOfGroupCombos;
-//     vector<string> Groups, outputNames, Sets;
-//     int processors;
-//     string groups, sets, calc, sharedfile, label, allLines, pickedGroups;
-//     vector<Calculator*> calculators;
-//     set<string> labels; //holds labels to be used
-//     int driver(int, int, vector<SharedRAbundVector*>, string);
-//     int driver(int, int, vector<string>, string, vector< vector<double> >&);
-//     int process(vector<SharedRAbundVector*>);       
 };
 
 #endif