reworked amova / homova / anosim

[mothur.git] / homovacommand.h

diff --git a/homovacommand.h b/homovacommand.h
index 55e4eac7b1a1efc7bac263186fd827bd72d19ad6..11f3c07fcebb96ddfe7a473aac8ccb0f234e167d 100644 (file)
--- a/homovacommand.h
+++ b/homovacommand.h
@@ -12,12 +12,9 @@
 
 
 #include "command.hpp"
-#include "inputdata.h"
-#include "sharedrabundvector.h"
-#include "validcalculator.h"
-#include "readphylipvector.h"
 
-class GlobalData;
+//class GlobalData;
+class GroupMap;
 
 class HomovaCommand : public Command {
        
@@ -33,35 +30,20 @@ public:
        void help();
        
 private:
-       struct linePair {
-               int start;
-               int num;
-               linePair(int i, int j) : start(i), num(j) {}
-       };
-       vector<linePair> lines;
-       
-       GlobalData* globaldata;
-       GroupMap* designMap;
+       double runHOMOVA(ofstream& , map<string, vector<int> >, double);
+       double calcSigleSSWithin(vector<int>);
+       double calcBValue(map<string, vector<int> >, vector<double>&);
+       map<string, vector<int> > getRandomizedGroups(map<string, vector<int> >);
+
+       bool abort;
        map<string, vector<string> > outputTypes;
-       
-       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 calcHomova(ofstream&, int, vector<string>);
-       map<string, double> calcWithinEach(vector< vector<double> >&, int, vector<string>, map<string, int>&);
-       double calcWithin(vector< vector<double> >&, int, vector<string>);
-       double calcTotal(int);
+       vector<string> outputNames;
+
+       string outputDir, inputDir, designFileName, phylipFileName;
+       GroupMap* designMap;
+       vector< vector<double> > distanceMatrix;
+       int iters;
+       double experimentwiseAlpha;
 };
 
 #endif
-
-