mods to amova command

[mothur.git] / amovacommand.h

diff --git a/amovacommand.h b/amovacommand.h
index 3b90b967437df2c0ad360675fc89537976dce989..d9fe1e6fe7e941c89ed65ffafce0f0ad2cc72c61 100644 (file)
--- a/amovacommand.h
+++ b/amovacommand.h
@@ -32,32 +32,39 @@ public:
        void help();
        
 private:
-       struct linePair {
-               int start;
-               int num;
-               linePair(int i, int j) : start(i), num(j) {}
-       };
-       vector<linePair> lines;
+       double runAMOVA(ofstream&, map<string, vector<int> >, double);
+       double calcSSWithin(map<string, vector<int> >&);
+       double calcSSTotal(map<string, vector<int> >&);
+       map<string, vector<int> > getRandomizedGroups(map<string, vector<int> >);
+
        
+       bool abort;
        GlobalData* globaldata;
-       GroupMap* designMap;
        map<string, vector<string> > outputTypes;
+       vector<string> outputNames;
+
+       string outputDir, inputDir, designFileName, phylipFileName;
+       GroupMap* designMap;
+       vector< vector<double> > distanceMatrix;
+       int iters;
+       double experimentwiseAlpha;
        
-       vector< vector<double> > matrix;
-       bool abort, allLines, pickedGroups;
-       set<string> labels; //holds labels to be used
-       string format, groups, label, outputDir, inputDir, designfile, sets, phylipfile, calc, sharedfile;
-       vector<string> Groups, outputNames, Sets;
-       vector< vector<string> > namesOfGroupCombos;
-       int iters, processors;
-       vector<Calculator*> calculators;
-       
-       int driver(int, int, vector<SharedRAbundVector*>, string);
-       int driver(int, int, vector<string>, string, vector< vector<double> >&);
-       int process(vector<SharedRAbundVector*>);
-       int calcAmova(ofstream&, int, vector<string>);
-       double calcWithin(vector< vector<double> >&, int, vector<string>);
-       double calcTotal(int);
+//     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